diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index 441e9cc8f03a6897117f22463229febe348489ec..cd8750bd84cdbb973fa55dbb6d7cda4572957406 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="21 Sep 2016 version">
+<META NAME="docnumber" CONTENT="26 Sep 2016 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@@ -21,7 +21,7 @@
<H1></H1>
LAMMPS Documentation :c,h3
-21 Sep 2016 version :c,h4
+26 Sep 2016 version :c,h4
Version info: :h4
diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt
index 3e18037a8343451ab359c825f175fc7cf24076af..91ec6793601d840491bc2ae5a7a3eb49a3144471 100644
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@@ -501,6 +501,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"bond/create"_fix_bond_create.html,
"bond/swap"_fix_bond_swap.html,
"box/relax"_fix_box_relax.html,
+"cmap"_fix_cmap.html,
"controller"_fix_controller.html,
"deform (k)"_fix_deform.html,
"deposit"_fix_deposit.html,
diff --git a/doc/src/Section_tools.txt b/doc/src/Section_tools.txt
index 3527d228de57603f55d5a2e697b93ea7aa4cde29..983be30f19791dc6551cd51858d932372c91bbfd 100644
--- a/doc/src/Section_tools.txt
+++ b/doc/src/Section_tools.txt
@@ -107,9 +107,10 @@ The ch2lmp sub-directory contains tools for converting files
back-and-forth between the CHARMM MD code and LAMMPS.
They are intended to make it easy to use CHARMM as a builder and as a
-post-processor for LAMMPS. Using charmm2lammps.pl, you can convert an
-ensemble built in CHARMM into its LAMMPS equivalent. Using
-lammps2pdb.pl you can convert LAMMPS atom dumps into pdb files.
+post-processor for LAMMPS. Using charmm2lammps.pl, you can convert a
+PDB file with associated CHARMM info, including CHARMM force field
+data, into its LAMMPS equivalent. Using lammps2pdb.pl you can convert
+LAMMPS atom dumps into PDB files.
See the README file in the ch2lmp sub-directory for more information.
diff --git a/doc/src/fix_cmap.txt b/doc/src/fix_cmap.txt
new file mode 100644
index 0000000000000000000000000000000000000000..924e6f5022364219795c3237d4011c06e6cb9b37
--- /dev/null
+++ b/doc/src/fix_cmap.txt
@@ -0,0 +1,132 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix cmap command :h3
+
+[Syntax:]
+
+fix ID group-ID cmap filename :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+cmap = style name of this fix command
+filename = force-field file with CMAP coefficients :ul
+
+[Examples:]
+
+fix myCMAP all cmap ../potentials/cmap36.data
+read_data proteinX.data fix myCMAP crossterm CMAP
+fix_modify myCMAP energy yes :pre
+
+[Description:]
+
+This command enables CMAP crossterms to be added to simulations which
+use the CHARMM force field. These are relevant for any CHARMM model
+of a peptide or protein sequences that is 3 or more amino-acid
+residues long; see "(Buck)"_#Buck and "(Brooks)"_#Brooks for details,
+including the analytic energy expressions for CMAP interactions. The
+CMAP crossterms add additional potential energy contributions to pairs
+of overlapping phi-psi dihedrals of amino-acids, which are important
+to properly represent their conformational behavior.
+
+The examples/cmap directory has a sample input script and data file
+for a small peptide, that illustrates use of the fix cmap command.
+
+As in the example above, this fix should be used before reading a data
+file that contains a listing of CMAP interactions. The {filename}
+specified should contain the CMAP parameters for a particular version
+of the CHARMM force field. Two such files are including in the
+lammps/potentials directory: charmm22.cmap and charmm36.cmap.
+
+The data file read by the "read_data" must contain the topology of all
+the CMAP interactions, similar to the topology data for bonds, angles,
+dihedrals, etc. Specically it should have a line like this
+in its header section:
+
+N crossterms :pre
+
+where N is the number of CMAP crossterms. It should also have a section
+in the body of the data file like this with N lines:
+
+CMAP :pre
+
+ 1 1 8 10 12 18 20
+ 2 5 18 20 22 25 27
+ ...
+ N 3 314 315 317 318 330 :pre
+
+The first column is an index from 1 to N to enumerate the CMAP terms;
+it is ignored by LAMMPS. The 2nd column is the "type" of the
+interaction; it is an index into the CMAP force field file. The
+remaining 5 columns are the atom IDs of the atoms in the two 4-atom
+dihedrals that overlap to create the CMAP 5-body interaction. Note
+that the "crossterm" and "CMAP" keywords for the header and body
+sections match those specified in the read_data command following the
+data file name; see the "read_data"_doc/read_data.html doc page for
+more details.
+
+A data file containing CMAP crossterms can be generated from a PDB
+file using the charmm2lammps.pl script in the tools/ch2lmp directory
+of the LAMMPS distribution. The script must be invoked with the
+optional "-cmap" flag to do this; see the tools/ch2lmp/README file for
+more information.
+
+The potential energy associated with CMAP interactions can be output
+as described below. It can also be included in the total potential
+energy of the system, as output by the
+"thermo_style"_thermo_style.html command, if the "fix_modify
+energy"_fix_modify.html command is used, as in the example above. See
+the note below about how to include the CMAP energy when performing an
+"energy minimization"_minimize.html.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.
+
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the potential "energy" of the CMAP interactions system's
+potential energy as part of "thermodynamic output"_thermo_style.html.
+
+This fix computes a global scalar which can be accessed by various
+"output commands"_Section_howto.html#howto_15. The scalar is the
+potential energy discussed above. The scalar value calculated by this
+fix is "extensive".
+
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the "minimize"_minimize.html command.
+
+NOTE: If you want the potential energy associated with the CMAP terms
+forces to be included in the total potential energy of the system (the
+quantity being minimized), you MUST enable the
+"fix_modify"_fix_modify.html {energy} option for this fix.
+
+[Restrictions:]
+
+This fix can only be used if LAMMPS was built with the MOLECULE
+package (which it is by default). See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info on packages.
+
+[Related commands:]
+
+"fix_modify"_fix_modify.html, "read_data"_read_data.html
+
+[Default:] none
+
+:line
+
+(Buck)
+Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36
+(2006).
+
+(Brooks)
+Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009).
diff --git a/examples/README b/examples/README
index 400d69aa2d17c9f679b2d8715193851c1b18acdc..462fa93e12f8bfa717687bbf28029c7689601097 100644
--- a/examples/README
+++ b/examples/README
@@ -61,6 +61,7 @@ sub-directories:
accelerate: use of all the various accelerator packages
balance: dynamic load balancing, 2d system
body: body particles, 2d system
+cmap: CMAP 5-body contributions to CHARMM force field
colloid: big colloid particles in a small particle solvent, 2d system
coreshell: adiabatic core/shell model
comb: models using the COMB potential
diff --git a/examples/cmap/charmm22.cmap b/examples/cmap/charmm22.cmap
new file mode 100644
index 0000000000000000000000000000000000000000..782dcc5dbf08a46d5b77a7d8fc0420e149e491a9
--- /dev/null
+++ b/examples/cmap/charmm22.cmap
@@ -0,0 +1,1022 @@
+# Title: charmm correction map
+
+# alanine map, type 1
+
+# -180
+0.126790 0.768700 0.971260 1.250970 2.121010
+2.695430 2.064440 1.764790 0.755870 -0.713470
+0.976130 -2.475520 -5.455650 -5.096450 -5.305850
+-3.975630 -3.088580 -2.784200 -2.677120 -2.646060
+-2.335350 -2.010440 -1.608040 -0.482250
+
+# -165
+-0.802290 1.377090 1.577020 1.872290 2.398990
+2.461630 2.333840 1.904070 1.061460 0.518400
+-0.116320 -3.575440 -5.284480 -5.160310 -4.196010
+-3.276210 -2.715340 -1.806200 -1.101780 -1.210320
+-1.008810 -0.637100 -1.603360 -1.776870
+
+# -150
+-0.634810 1.156210 1.624350 2.047200 2.653910
+2.691410 2.296420 1.960450 1.324930 2.038290
+-1.151510 -3.148610 -4.058280 -4.531850 -3.796370
+-2.572090 -1.727250 -0.961410 -0.282910 -0.479120
+-1.039340 -1.618060 -1.725460 -1.376360
+
+# -135
+0.214000 1.521370 1.977440 2.377950 2.929470
+2.893410 2.435810 2.162970 1.761500 1.190090
+-1.218610 -2.108900 -2.976100 -3.405340 -2.768440
+-1.836030 -0.957950 0.021790 -0.032760 -0.665880
+-1.321170 -1.212320 -0.893170 -0.897040
+
+# -120
+0.873950 1.959160 2.508990 2.841100 3.698960
+3.309330 2.614300 2.481720 2.694660 1.082440
+-0.398320 -1.761800 -2.945110 -3.294690 -2.308300
+-0.855480 -0.087320 0.439040 0.691880 -0.586330
+-1.027210 -0.976640 -0.467580 0.104020
+
+# -105
+1.767380 2.286650 2.818030 3.065500 3.370620
+3.397440 2.730310 2.878790 2.542010 1.545240
+-0.092150 -1.694440 -2.812310 -2.802430 -1.856360
+-0.306240 -0.122440 0.444680 0.810150 -0.058630
+-0.270290 -0.178830 0.202360 0.493810
+
+# -90
+1.456010 2.743180 2.589450 3.046230 3.451510
+3.319160 3.052900 3.873720 2.420650 0.949100
+0.008370 -1.382980 -2.138930 -2.087380 -1.268300
+-0.494370 0.267580 0.908250 0.537520 0.306260
+0.069540 0.097460 0.263060 0.603220
+
+# -75
+1.396790 3.349090 2.180920 2.942960 3.814070
+3.675800 3.555310 3.887290 2.101260 -0.190940
+-0.732240 -1.382040 -0.673880 -0.817390 -0.826980
+-0.111800 0.053710 0.296400 0.692240 0.428960
+-0.036100 -0.033820 -0.194300 0.400210
+
+# -60
+0.246650 1.229980 1.716960 3.168570 4.208190
+4.366860 4.251080 3.348110 0.997540 -1.287540
+-1.179900 -0.684300 -0.853660 -1.158760 -0.347550
+0.114810 0.242800 0.322420 0.370140 -0.374950
+-0.676940 -1.323430 -1.366650 -0.218770
+
+# -45
+-1.196730 0.078060 2.347410 4.211350 5.376000
+5.364940 4.355200 2.436510 0.408470 -0.590840
+-0.435960 -0.501210 -0.822230 -0.607210 0.057910
+0.246580 -0.070570 0.379430 0.247770 -0.571680
+-1.282910 -1.715770 -1.839820 -1.987110
+
+# -30
+-1.174720 1.067030 4.180460 6.741610 6.070770
+4.781470 2.758340 1.295810 0.571150 -0.196480
+0.251860 -0.732140 1.289360 1.497590 1.890550
+2.198490 0.169290 0.534000 0.331780 -1.276320
+-2.550070 -3.312150 -3.136670 -2.642260
+
+# -15
+0.293590 5.588070 3.732620 3.217620 3.272450
+2.492320 1.563700 1.356760 0.831410 0.630170
+1.591970 0.821920 0.486070 0.715760 0.996020
+1.591580 -0.367400 0.181770 -0.613920 -2.267900
+-3.516460 -3.597700 -3.043340 -1.765020
+
+# 0
+2.832310 0.787990 0.323280 0.479230 0.628600
+0.976330 1.238750 1.671950 1.645480 2.520340
+1.606970 0.776350 0.119780 0.070390 0.121170
+-1.569230 -1.213010 -1.846360 -2.744510 -3.792530
+-3.934880 -3.615930 -2.675750 -0.924170
+
+# 15
+-0.778340 -1.912680 -2.052140 -1.846280 -1.047430
+0.183400 1.682950 2.223500 1.358370 2.448660
+1.436920 0.678570 -0.237060 -0.535320 -0.790380
+-2.182580 -3.251140 -4.195110 -4.269270 -3.908210
+-3.455620 -2.773970 1.755370 0.313410
+
+# 30
+-2.963810 -3.483730 -3.517080 -2.724860 -1.405510
+0.336200 1.428450 1.394630 0.970370 2.462720
+1.522430 0.553620 -0.407380 -1.482950 -3.613920
+-4.159810 -4.945580 -4.784040 -3.764540 -2.959140
+-1.963850 -1.071260 -1.599580 -2.445320
+
+# 45
+-4.029070 -3.932660 -3.558480 -2.513980 -1.037320
+0.362000 0.814380 0.754110 0.502370 1.903420
+0.770220 -0.416420 -3.286310 -3.875270 -4.907800
+-5.704430 -5.645660 -4.396040 -2.865450 -2.368170
+-2.860490 -3.416560 -3.666490 -3.859070
+
+# 60
+-3.338270 -2.960220 -2.311700 -1.272890 -0.246470
+0.722610 0.668070 0.438130 2.395330 1.632470
+-2.041450 -3.218100 -3.915080 -4.852510 -5.696500
+-6.314370 -5.683690 -4.170620 -3.141000 -3.508820
+-3.756430 -3.640810 -3.640430 -3.550690
+
+# 75
+-2.244860 -1.632100 -1.000640 -0.170440 0.526440
+0.823710 0.517140 -0.013120 -0.370910 -1.213720
+-2.305650 -3.420580 -4.484960 -5.693140 -6.199150
+-6.253870 -5.211310 -4.174380 -3.685150 -4.151360
+-4.161970 -3.725150 -3.715310 -2.606760
+
+# 90
+-1.720840 -1.177830 -0.428430 0.277730 0.807900
+0.803260 0.482510 -0.336900 -0.786270 -1.774070
+-2.793220 -3.828560 -5.211800 -6.636850 -6.989940
+-6.108800 -5.452410 -3.911450 -4.321000 -4.587240
+-4.102610 -3.772820 -3.157300 -2.648390
+
+# 105
+-1.850640 -1.092420 -0.445020 0.128490 1.005520
+0.884820 0.485850 -0.218470 -0.857670 -1.682330
+-3.014400 -4.481110 -6.053510 -6.865400 -6.871130
+-5.728240 -3.912230 -4.802110 -5.034640 -4.715990
+-4.601080 -4.086220 -3.274630 -2.410940
+
+# 120
+-1.969230 -1.116650 -0.540250 -0.150330 0.763520
+1.038890 0.758480 0.313530 -0.333050 -1.872770
+-3.366270 -5.008260 -6.124810 -7.034830 -6.724320
+-3.700200 -4.510620 -5.185650 -5.361620 -4.847490
+-4.444320 -4.004260 -3.415720 -2.751230
+
+# 135
+-2.111250 -1.168960 -0.322790 -0.006920 0.316660
+1.086270 0.939170 0.625340 -0.166360 -1.830310
+-3.469470 -4.946030 -6.112560 -1.915580 -4.047310
+-4.996740 -4.996730 -4.842690 -4.886620 -4.300540
+-4.494620 -4.442210 -4.163570 -3.183510
+
+# 150
+-1.757590 -0.403620 0.023920 0.362390 0.634520
+1.264920 1.361360 0.948420 -0.073680 -1.483560
+-3.152820 1.835120 -1.762860 -5.093660 -5.744830
+-5.390070 -4.783930 -4.190630 -4.115420 -4.042280
+-4.125570 -4.028550 -4.026100 -2.937910
+
+# 165
+-0.810590 -0.071500 0.378890 0.543310 1.277880
+1.641310 1.698840 1.519950 0.631950 -1.088670
+-2.736530 -0.735240 -4.563830 -6.408350 -5.889450
+-5.141750 -4.194970 -3.666490 -3.843450 -3.818830
+-3.826180 -3.596820 -2.994790 -2.231020
+
+# alanine before proline map, type 2
+
+# -180
+0.126790 0.768700 0.971260 1.250970 2.121010
+2.695430 2.064440 1.764790 0.755870 -0.713470
+0.976130 -2.475520 -5.455650 -5.096450 -5.305850
+-3.975630 -3.088580 -2.784200 -2.677120 -2.646060
+-2.335350 -2.010440 -1.608040 -0.482250
+
+# -165
+-0.802290 1.377090 1.577020 1.872290 2.398990
+2.461630 2.333840 1.904070 1.061460 0.518400
+-0.116320 -3.575440 -5.284480 -5.160310 -4.196010
+-3.276210 -2.715340 -1.806200 -1.101780 -1.210320
+-1.008810 -0.637100 -1.603360 -1.776870
+
+# -150
+-0.634810 1.156210 1.624350 2.047200 2.653910
+2.691410 2.296420 1.960450 1.324930 2.038290
+-1.151510 -3.148610 -4.058280 -4.531850 -3.796370
+-2.572090 -1.727250 -0.961410 -0.282910 -0.479120
+-1.039340 -1.618060 -1.725460 -1.376360
+
+# -135
+0.214000 1.521370 1.977440 2.377950 2.929470
+2.893410 2.435810 2.162970 1.761500 1.190090
+-1.218610 -2.108900 -2.976100 -3.405340 -2.768440
+-1.836030 -0.957950 0.021790 -0.032760 -0.665880
+-1.321170 -1.212320 -0.893170 -0.897040
+
+# -120
+0.873950 1.959160 2.508990 2.841100 3.698960
+3.309330 2.614300 2.481720 2.694660 1.082440
+-0.398320 -1.761800 -2.945110 -3.294690 -2.308300
+-0.855480 -0.087320 0.439040 0.691880 -0.586330
+-1.027210 -0.976640 -0.467580 0.104020
+
+# -105
+1.767380 2.286650 2.818030 3.065500 3.370620
+3.397440 2.730310 2.878790 2.542010 1.545240
+-0.092150 -1.694440 -2.812310 -2.802430 -1.856360
+-0.306240 -0.122440 0.444680 0.810150 -0.058630
+-0.270290 -0.178830 0.202360 0.493810
+
+# -90
+1.456010 2.743180 2.589450 3.046230 3.451510
+3.319160 3.052900 3.873720 2.420650 0.949100
+0.008370 -1.382980 -2.138930 -2.087380 -1.268300
+-0.494370 0.267580 0.908250 0.537520 0.306260
+0.069540 0.097460 0.263060 0.603220
+
+# -75
+1.396790 3.349090 2.180920 2.942960 3.814070
+3.675800 3.555310 3.887290 2.101260 -0.190940
+-0.732240 -1.382040 -0.673880 -0.817390 -0.826980
+-0.111800 0.053710 0.296400 0.692240 0.428960
+-0.036100 -0.033820 -0.194300 0.400210
+
+# -60
+0.246650 1.229980 1.716960 3.168570 4.208190
+4.366860 4.251080 3.348110 0.997540 -1.287540
+-1.179900 -0.684300 -0.853660 -1.158760 -0.347550
+0.114810 0.242800 0.322420 0.370140 -0.374950
+-0.676940 -1.323430 -1.366650 -0.218770
+
+# -45
+-1.196730 0.078060 2.347410 4.211350 5.376000
+5.364940 4.355200 2.436510 0.408470 -0.590840
+-0.435960 -0.501210 -0.822230 -0.607210 0.057910
+0.246580 -0.070570 0.379430 0.247770 -0.571680
+-1.282910 -1.715770 -1.839820 -1.987110
+
+# -30
+-1.174720 1.067030 4.180460 6.741610 6.070770
+4.781470 2.758340 1.295810 0.571150 -0.196480
+0.251860 -0.732140 1.289360 1.497590 1.890550
+2.198490 0.169290 0.534000 0.331780 -1.276320
+-2.550070 -3.312150 -3.136670 -2.642260
+
+# -15
+0.293590 5.588070 3.732620 3.217620 3.272450
+2.492320 1.563700 1.356760 0.831410 0.630170
+1.591970 0.821920 0.486070 0.715760 0.996020
+1.591580 -0.367400 0.181770 -0.613920 -2.267900
+-3.516460 -3.597700 -3.043340 -1.765020
+
+# 0
+2.832310 0.787990 0.323280 0.479230 0.628600
+0.976330 1.238750 1.671950 1.645480 2.520340
+1.606970 0.776350 0.119780 0.070390 0.121170
+-1.569230 -1.213010 -1.846360 -2.744510 -3.792530
+-3.934880 -3.615930 -2.675750 -0.924170
+
+# 15
+-0.778340 -1.912680 -2.052140 -1.846280 -1.047430
+0.183400 1.682950 2.223500 1.358370 2.448660
+1.436920 0.678570 -0.237060 -0.535320 -0.790380
+-2.182580 -3.251140 -4.195110 -4.269270 -3.908210
+-3.455620 -2.773970 1.755370 0.313410
+
+# 30
+-2.963810 -3.483730 -3.517080 -2.724860 -1.405510
+0.336200 1.428450 1.394630 0.970370 2.462720
+1.522430 0.553620 -0.407380 -1.482950 -3.613920
+-4.159810 -4.945580 -4.784040 -3.764540 -2.959140
+-1.963850 -1.071260 -1.599580 -2.445320
+
+# 45
+-4.029070 -3.932660 -3.558480 -2.513980 -1.037320
+0.362000 0.814380 0.754110 0.502370 1.903420
+0.770220 -0.416420 -3.286310 -3.875270 -4.907800
+-5.704430 -5.645660 -4.396040 -2.865450 -2.368170
+-2.860490 -3.416560 -3.666490 -3.859070
+
+# 60
+-3.338270 -2.960220 -2.311700 -1.272890 -0.246470
+0.722610 0.668070 0.438130 2.395330 1.632470
+-2.041450 -3.218100 -3.915080 -4.852510 -5.696500
+-6.314370 -5.683690 -4.170620 -3.141000 -3.508820
+-3.756430 -3.640810 -3.640430 -3.550690
+
+# 75
+-2.244860 -1.632100 -1.000640 -0.170440 0.526440
+0.823710 0.517140 -0.013120 -0.370910 -1.213720
+-2.305650 -3.420580 -4.484960 -5.693140 -6.199150
+-6.253870 -5.211310 -4.174380 -3.685150 -4.151360
+-4.161970 -3.725150 -3.715310 -2.606760
+
+# 90
+-1.720840 -1.177830 -0.428430 0.277730 0.807900
+0.803260 0.482510 -0.336900 -0.786270 -1.774070
+-2.793220 -3.828560 -5.211800 -6.636850 -6.989940
+-6.108800 -5.452410 -3.911450 -4.321000 -4.587240
+-4.102610 -3.772820 -3.157300 -2.648390
+
+# 105
+-1.850640 -1.092420 -0.445020 0.128490 1.005520
+0.884820 0.485850 -0.218470 -0.857670 -1.682330
+-3.014400 -4.481110 -6.053510 -6.865400 -6.871130
+-5.728240 -3.912230 -4.802110 -5.034640 -4.715990
+-4.601080 -4.086220 -3.274630 -2.410940
+
+# 120
+-1.969230 -1.116650 -0.540250 -0.150330 0.763520
+1.038890 0.758480 0.313530 -0.333050 -1.872770
+-3.366270 -5.008260 -6.124810 -7.034830 -6.724320
+-3.700200 -4.510620 -5.185650 -5.361620 -4.847490
+-4.444320 -4.004260 -3.415720 -2.751230
+
+# 135
+-2.111250 -1.168960 -0.322790 -0.006920 0.316660
+1.086270 0.939170 0.625340 -0.166360 -1.830310
+-3.469470 -4.946030 -6.112560 -1.915580 -4.047310
+-4.996740 -4.996730 -4.842690 -4.886620 -4.300540
+-4.494620 -4.442210 -4.163570 -3.183510
+
+# 150
+-1.757590 -0.403620 0.023920 0.362390 0.634520
+1.264920 1.361360 0.948420 -0.073680 -1.483560
+-3.152820 1.835120 -1.762860 -5.093660 -5.744830
+-5.390070 -4.783930 -4.190630 -4.115420 -4.042280
+-4.125570 -4.028550 -4.026100 -2.937910
+
+# 165
+-0.810590 -0.071500 0.378890 0.543310 1.277880
+1.641310 1.698840 1.519950 0.631950 -1.088670
+-2.736530 -0.735240 -4.563830 -6.408350 -5.889450
+-5.141750 -4.194970 -3.666490 -3.843450 -3.818830
+-3.826180 -3.596820 -2.994790 -2.231020
+
+# proline, type 3
+
+# -180.00
+-4.60660 -4.28920 -4.51420 -5.49210 -6.65460
+-7.18530 -7.63320 -8.41920 -9.12510 -8.97830
+-9.02750 -8.88890 -8.61060 -8.10240 -7.96680
+-7.98860 -7.96190 -7.56330 -7.73950 -8.31580
+-9.33380 -9.61880 -7.91860 -6.00570
+
+# -165.00
+-3.21030 -2.90350 -3.04340 -3.83720 -4.92360
+-5.41790 -5.78320 -6.62490 -7.17820 -7.59500
+-7.60980 -7.39440 -6.68190 -6.24950 -5.83810
+-5.90510 -5.57900 -4.89950 -5.18840 -6.13180
+-6.93510 -7.49160 -5.84410 -4.48890
+
+# -150.00
+-2.23750 -2.26520 -2.55120 -3.67610 -4.61620
+-5.01560 -5.36920 -5.93110 -6.16820 -6.48830
+-6.54220 -6.14310 -5.33350 -4.85090 -4.50790
+-4.44050 -4.34380 -4.13820 -4.35620 -5.24880
+-6.05280 -6.18610 -4.80390 -3.41730
+
+# -135.00
+-2.12830 -2.02010 -2.90220 -3.88240 -4.63610
+-5.02000 -5.46090 -5.79830 -5.63220 -6.41490
+-6.20330 -5.57550 -4.58160 -4.15850 -4.00710
+-3.95020 -3.76880 -4.09690 -4.52680 -5.33410
+-5.97380 -5.68710 -4.70040 -3.33790
+
+# -120.00
+-2.20610 -2.22370 -2.85110 -3.55370 -4.33320
+-4.57860 -4.95030 -5.23950 -5.37730 -6.14740
+-5.98660 -5.17760 -4.16090 -3.78450 -3.83210
+-3.86590 -4.21340 -4.26250 -4.16200 -4.62160
+-5.47440 -5.38280 -4.39100 -3.16760
+
+# -105.00
+-1.32980 -1.44660 -2.00420 -2.84440 -3.31580
+-3.15410 -2.83060 -3.04980 -4.04810 -5.02030
+-4.84090 -3.88520 -2.79540 -2.49190 -2.65990
+-3.34670 -3.60580 -3.76970 -4.07430 -4.21930
+-4.66740 -4.23940 -3.37160 -2.10050
+
+# -90.00
+-0.27400 -0.41780 -0.92340 -1.48470 -1.84370
+-1.42480 -1.14210 -1.83280 -2.97900 -3.57000
+-3.33310 -2.24200 -1.31350 -0.96640 0.38300
+-0.57540 -0.74080 -0.59130 -0.41960 -2.64120
+-3.25380 -2.85540 -2.09970 -0.95660
+
+# -75.00
+ 0.26880 0.18190 0.00300 -0.45390 -0.24210
+ 0.21240 0.33320 -0.95520 -2.17670 -2.66490
+-2.24910 -1.35480 -0.35030 1.84000 0.81880
+ 0.41530 0.58460 0.65350 0.54960 0.41300
+ 0.23350 -2.13490 -1.54900 -0.38340
+
+# -60.00
+-0.48820 -0.40730 -0.25210 -0.20490 0.53370
+ 1.05990 0.72540 -0.68300 -2.10190 -2.83530
+-2.55500 -1.33940 -0.24710 1.63190 1.10600
+ 1.16350 1.30720 1.49310 1.16160 0.99320
+-2.33360 -2.59380 -2.01110 -1.46840
+
+# -45.00
+-2.41010 -1.30740 -0.85960 -0.06830 0.20500
+ 0.00650 -0.59750 -2.39820 -3.98270 -4.46610
+-3.51230 -1.99330 0.96050 0.80870 0.64450
+ 0.82590 1.00550 1.28110 0.96670 -2.71140
+-4.18330 -4.83370 -4.49950 -3.47920
+
+# -30.00
+-3.46300 -2.06680 -0.84260 -0.70440 -1.85140
+-2.59990 -3.62600 -5.08050 -6.35480 -6.08340
+-4.78650 -1.24210 -0.81660 -0.60170 -0.50040
+-0.41020 -0.28450 -0.14620 -3.14950 -5.16280
+-6.81940 -7.52060 -7.12480 -5.49420
+
+# -15.00
+-2.70550 -1.11410 -0.82120 -3.80470 -4.50780
+-4.64960 -5.78530 -7.04450 -7.30810 -6.56450
+-3.47860 -2.68630 -1.78120 -1.48400 -1.45930
+-1.43060 -5.75320 -2.72500 -6.45790 -8.16530
+-9.86330 -9.80710 -8.62670 -6.49690
+
+# 0.00
+-2.73190 -3.83060 -5.26960 -5.91610 -6.71690
+-7.05420 -7.77520 -7.81220 -7.54160 -4.98400
+-5.05070 -4.28910 -3.78740 -3.64600 -3.91990
+-3.55740 -3.03470 -5.78910 -7.02720 -8.04090
+-8.60950 -8.27740 -7.10120 -5.12040
+
+# 15.00
+-3.17420 -4.66830 -6.17790 -7.26760 -8.22560
+-8.32120 -7.64880 -7.00240 -4.77210 -5.65380
+-5.36790 -4.43640 -4.37720 -4.45280 -4.47980
+-4.07260 -6.75420 -7.56910 -7.95830 -7.87760
+-7.88160 -7.29010 -7.15600 -5.19260
+
+# 30.00
+-2.96240 -4.87720 -6.64930 -7.95180 -8.47610
+-7.49950 -6.26260 -6.35040 -4.34190 -4.49790
+-4.27480 -1.75620 -3.89990 -3.81400 -3.99610
+-6.66430 -7.66400 -7.80660 -7.21980 -6.83750
+-6.88220 -7.10200 -5.10200 -2.38920
+
+# 45
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 60
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 75
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 90
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 105
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 120
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 135
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 150
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 165
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 2 adjacent prolines, type 4
+
+# -180.00
+-4.60660 -4.28920 -4.51420 -5.49210 -6.65460
+-7.18530 -7.63320 -8.41920 -9.12510 -8.97830
+-9.02750 -8.88890 -8.61060 -8.10240 -7.96680
+-7.98860 -7.96190 -7.56330 -7.73950 -8.31580
+-9.33380 -9.61880 -7.91860 -6.00570
+
+# -165.00
+-3.21030 -2.90350 -3.04340 -3.83720 -4.92360
+-5.41790 -5.78320 -6.62490 -7.17820 -7.59500
+-7.60980 -7.39440 -6.68190 -6.24950 -5.83810
+-5.90510 -5.57900 -4.89950 -5.18840 -6.13180
+-6.93510 -7.49160 -5.84410 -4.48890
+
+# -150.00
+-2.23750 -2.26520 -2.55120 -3.67610 -4.61620
+-5.01560 -5.36920 -5.93110 -6.16820 -6.48830
+-6.54220 -6.14310 -5.33350 -4.85090 -4.50790
+-4.44050 -4.34380 -4.13820 -4.35620 -5.24880
+-6.05280 -6.18610 -4.80390 -3.41730
+
+# -135.00
+-2.12830 -2.02010 -2.90220 -3.88240 -4.63610
+-5.02000 -5.46090 -5.79830 -5.63220 -6.41490
+-6.20330 -5.57550 -4.58160 -4.15850 -4.00710
+-3.95020 -3.76880 -4.09690 -4.52680 -5.33410
+-5.97380 -5.68710 -4.70040 -3.33790
+
+# -120.00
+-2.20610 -2.22370 -2.85110 -3.55370 -4.33320
+-4.57860 -4.95030 -5.23950 -5.37730 -6.14740
+-5.98660 -5.17760 -4.16090 -3.78450 -3.83210
+-3.86590 -4.21340 -4.26250 -4.16200 -4.62160
+-5.47440 -5.38280 -4.39100 -3.16760
+
+# -105.00
+-1.32980 -1.44660 -2.00420 -2.84440 -3.31580
+-3.15410 -2.83060 -3.04980 -4.04810 -5.02030
+-4.84090 -3.88520 -2.79540 -2.49190 -2.65990
+-3.34670 -3.60580 -3.76970 -4.07430 -4.21930
+-4.66740 -4.23940 -3.37160 -2.10050
+
+# -90.00
+-0.27400 -0.41780 -0.92340 -1.48470 -1.84370
+-1.42480 -1.14210 -1.83280 -2.97900 -3.57000
+-3.33310 -2.24200 -1.31350 -0.96640 0.38300
+-0.57540 -0.74080 -0.59130 -0.41960 -2.64120
+-3.25380 -2.85540 -2.09970 -0.95660
+
+# -75.00
+ 0.26880 0.18190 0.00300 -0.45390 -0.24210
+ 0.21240 0.33320 -0.95520 -2.17670 -2.66490
+-2.24910 -1.35480 -0.35030 1.84000 0.81880
+ 0.41530 0.58460 0.65350 0.54960 0.41300
+ 0.23350 -2.13490 -1.54900 -0.38340
+
+# -60.00
+-0.48820 -0.40730 -0.25210 -0.20490 0.53370
+ 1.05990 0.72540 -0.68300 -2.10190 -2.83530
+-2.55500 -1.33940 -0.24710 1.63190 1.10600
+ 1.16350 1.30720 1.49310 1.16160 0.99320
+-2.33360 -2.59380 -2.01110 -1.46840
+
+# -45.00
+-2.41010 -1.30740 -0.85960 -0.06830 0.20500
+ 0.00650 -0.59750 -2.39820 -3.98270 -4.46610
+-3.51230 -1.99330 0.96050 0.80870 0.64450
+ 0.82590 1.00550 1.28110 0.96670 -2.71140
+-4.18330 -4.83370 -4.49950 -3.47920
+
+# -30.00
+-3.46300 -2.06680 -0.84260 -0.70440 -1.85140
+-2.59990 -3.62600 -5.08050 -6.35480 -6.08340
+-4.78650 -1.24210 -0.81660 -0.60170 -0.50040
+-0.41020 -0.28450 -0.14620 -3.14950 -5.16280
+-6.81940 -7.52060 -7.12480 -5.49420
+
+# -15.00
+-2.70550 -1.11410 -0.82120 -3.80470 -4.50780
+-4.64960 -5.78530 -7.04450 -7.30810 -6.56450
+-3.47860 -2.68630 -1.78120 -1.48400 -1.45930
+-1.43060 -5.75320 -2.72500 -6.45790 -8.16530
+-9.86330 -9.80710 -8.62670 -6.49690
+
+# 0.00
+-2.73190 -3.83060 -5.26960 -5.91610 -6.71690
+-7.05420 -7.77520 -7.81220 -7.54160 -4.98400
+-5.05070 -4.28910 -3.78740 -3.64600 -3.91990
+-3.55740 -3.03470 -5.78910 -7.02720 -8.04090
+-8.60950 -8.27740 -7.10120 -5.12040
+
+# 15.00
+-3.17420 -4.66830 -6.17790 -7.26760 -8.22560
+-8.32120 -7.64880 -7.00240 -4.77210 -5.65380
+-5.36790 -4.43640 -4.37720 -4.45280 -4.47980
+-4.07260 -6.75420 -7.56910 -7.95830 -7.87760
+-7.88160 -7.29010 -7.15600 -5.19260
+
+# 30.00
+-2.96240 -4.87720 -6.64930 -7.95180 -8.47610
+-7.49950 -6.26260 -6.35040 -4.34190 -4.49790
+-4.27480 -1.75620 -3.89990 -3.81400 -3.99610
+-6.66430 -7.66400 -7.80660 -7.21980 -6.83750
+-6.88220 -7.10200 -5.10200 -2.38920
+
+# 45
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 60
+0.000000 0.000000 0.000000 0.000000 0.000000
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+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 75
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 90
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 105
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 120
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 135
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 150
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 165
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# glycine map, type 5
+
+# -180
+-0.549160 -0.535500 -0.588110 -0.754620 -0.679290
+-0.038150 0.298460 0.326040 -0.375610 -1.704360
+-3.061280 -3.956460 -3.576280 -1.038930 2.012450
+-1.714610 -0.377660 0.317310 0.294580 -0.042920
+-0.676620 -0.744600 -0.586590 -0.554770
+
+# -165
+-0.709450 -0.896700 -0.990850 -1.319240 -0.940260
+-0.126160 0.329180 0.258100 -0.534910 -1.715700
+-2.780320 -3.153350 -1.636020 1.822690 -2.675640
+-1.810120 -0.410680 0.180860 0.196710 -0.000430
+-0.271890 -0.462500 -0.348750 -0.477660
+
+# -150
+-1.224850 -1.482430 -1.665900 -1.656770 -1.119780
+-1.642540 -0.054220 -0.290670 -0.887080 -1.626260
+-2.165440 -1.546500 0.753400 -2.949180 -2.225630
+-1.664160 -0.628990 0.000490 0.033160 -0.092820
+-0.339050 -0.563330 -0.794980 -0.710760
+
+# -135
+-1.787640 -2.117750 -2.143020 -1.803720 -1.567160
+-0.886880 -0.801350 -0.851590 -1.020630 -1.337360
+-1.062570 0.338010 -4.372310 -2.435890 -2.220710
+-1.718060 -0.758950 -0.207560 0.100910 -0.055650
+-0.288370 -0.880610 -1.267450 -1.465530
+
+# -120
+-2.348270 -2.593790 -2.596140 -2.364070 -1.970070
+-1.705860 -1.435540 -1.289220 -1.358170 -0.975570
+-3.514390 -4.283210 -3.975820 -3.215190 -2.394430
+-1.455320 -0.553910 -0.158900 -0.173830 -0.297950
+-0.661220 -1.068330 -1.601800 -1.914850
+
+# -105
+-2.788800 -3.079570 -3.178150 -3.013710 -2.626630
+-2.266680 -1.951490 -1.681850 -1.195390 -2.567680
+-3.632800 -4.748210 -4.662850 -4.255190 -2.776760
+-1.695490 -0.893140 -0.633810 -0.467320 -0.540540
+-0.950190 -1.401500 -1.959970 -2.412680
+
+# -90
+-3.857170 -3.713610 -3.902110 -3.611370 -3.040850
+-2.406460 -1.975250 -1.452040 -0.971860 -2.808170
+-4.181160 -4.981430 -5.446890 -4.359900 -2.864390
+-1.898510 -1.139090 -0.971340 -1.065550 -1.020680
+-1.141350 -1.794480 -2.420970 -2.939990
+
+# -75
+-4.987770 -4.995210 -4.485310 -3.892550 -3.228630
+-2.345360 -1.664160 -1.105500 -1.945510 -3.715530
+-4.492140 -5.536170 -5.708500 -3.675410 -2.986660
+-1.859410 -0.756620 -1.269930 -1.312730 -1.607440
+-1.892510 -2.659400 -3.347950 -3.970600
+
+# -60
+-6.183650 -5.456080 -4.878940 -4.000820 -2.683230
+-2.067520 -1.094850 -1.119790 -2.962910 -3.687830
+-4.993340 -4.666260 -3.796280 -3.374140 -2.495430
+-1.453990 -0.877560 -1.002930 -1.337310 -2.431360
+-2.948140 -4.008100 -4.821040 -5.565810
+
+# -45
+-6.755760 -5.850030 -4.362190 -2.714090 -1.708710
+-0.526660 -0.536700 -2.037170 -3.892650 -4.558570
+-4.237410 -3.735160 -3.688580 -3.009910 -2.112940
+-1.455400 -0.925490 -1.121840 -1.561900 -2.751370
+-4.094860 -5.207530 -6.128530 -6.613030
+
+# -30
+-5.716250 -4.434060 -2.788600 -0.974400 -0.729200
+-0.904940 -1.833540 -3.017700 -3.313450 -3.336010
+-3.181640 -3.594720 -1.231370 -0.603790 0.128810
+-1.222610 -0.909150 -0.837700 -1.346820 -3.040880
+-4.731110 -5.844860 -6.428460 -6.424880
+
+# -15
+-3.991110 -2.046000 0.082550 -2.676110 -2.828500
+-2.596640 -2.843330 -3.011480 -2.312640 -2.405980
+-3.086210 -1.164620 -1.231660 -0.871900 -0.348980
+-1.735900 -0.914150 -0.484520 -1.818040 -3.602550
+-5.330320 -5.992270 -5.588080 -5.408360
+
+# 0
+-1.147060 -3.317730 -4.305100 -4.615200 -4.533780
+-3.622950 -2.832800 -1.872810 -1.144300 -1.994070
+-0.741980 -1.115010 -1.229250 -1.103680 -0.742430
+-1.973970 -1.070020 -1.802220 -2.712770 -3.624130
+-4.537100 -4.619970 -4.310890 -3.318290
+
+# 15
+-3.997710 -5.408360 -5.588080 -5.992270 -5.330320
+-3.602550 -1.818040 -0.484520 -0.914150 -1.735900
+-0.348980 -0.871900 -1.231660 -1.164620 -3.086210
+-2.405980 -2.312640 -3.011480 -2.843330 -2.596640
+-2.828500 -2.676110 0.082550 -2.046000
+
+# 30
+-5.710850 -6.424880 -6.428460 -5.844860 -4.731110
+-3.040880 -1.346820 -0.837700 -0.909150 -1.222610
+0.128810 -0.603790 -1.231370 -3.594720 -3.181640
+-3.336010 -3.313450 -3.017700 -1.833540 -0.904940
+-0.729200 -0.974400 -2.788600 -4.434060
+
+# 45
+-6.754940 -6.613030 -6.128530 -5.207530 -4.094860
+-2.751370 -1.561900 -1.121840 -0.925490 -1.455400
+-2.112940 -3.009910 -3.688580 -3.735160 -4.237410
+-4.558570 -3.892650 -2.037170 -0.536700 -0.526660
+-1.708710 -2.714090 -4.362190 -5.850030
+
+# 60
+-6.188070 -5.565810 -4.821040 -4.008100 -2.948140
+-2.431360 -1.337310 -1.002930 -0.877560 -1.453990
+-2.495430 -3.374140 -3.796280 -4.666260 -4.993340
+-3.687830 -2.962910 -1.119790 -1.094850 -2.067520
+-2.683230 -4.000820 -4.878940 -5.456080
+
+# 75
+-4.986080 -3.970600 -3.347950 -2.659400 -1.892510
+-1.607440 -1.312730 -1.269930 -0.756620 -1.859410
+-2.986660 -3.675410 -5.708500 -5.536170 -4.492140
+-3.715530 -1.945510 -1.105500 -1.664160 -2.345360
+-3.228630 -3.892550 -4.485310 -4.995210
+
+# 90
+-3.879190 -2.939990 -2.420970 -1.794480 -1.141350
+-1.020680 -1.065550 -0.971340 -1.139090 -1.898510
+-2.864390 -4.359900 -5.446890 -4.981430 -4.181160
+-2.808170 -0.971860 -1.452040 -1.975250 -2.406460
+-3.040850 -3.611370 -3.902110 -3.713610
+
+# 105
+-2.793280 -2.412680 -1.959970 -1.401500 -0.950190
+-0.540540 -0.467320 -0.633810 -0.893140 -1.695490
+-2.776760 -4.255190 -4.662850 -4.448210 -3.332800
+-2.567680 -1.195390 -1.681850 -1.951490 -2.266680
+-2.626630 -3.013710 -3.178150 -3.079570
+
+# 120
+-2.330190 -1.914850 -1.601800 -1.068330 -0.661220
+-0.297950 -0.173830 -0.158900 -0.553910 -1.455320
+-2.394430 -3.215190 -3.975820 -3.783210 -3.014390
+-0.975570 -1.358170 -1.289220 -1.435540 -1.705860
+-1.970070 -2.364070 -2.596140 -2.593790
+
+# 135
+-1.796120 -1.465530 -1.267450 -0.880610 -0.288370
+-0.055650 0.100910 -0.207560 -0.758950 -1.718060
+-2.220710 -2.435890 -4.372310 0.338010 -1.062570
+-1.337360 -1.020630 -0.851590 -0.801350 -0.886880
+-1.567160 -1.803720 -2.143020 -2.117750
+
+# 150
+-1.263610 -0.710760 -0.794980 -0.563330 -0.339050
+-0.092820 0.033160 0.000490 -0.628990 -1.664160
+-2.225630 -2.949180 0.753400 -1.546500 -2.165440
+-1.626260 -0.887080 -0.290670 -0.054220 -1.642540
+-1.119780 -1.656770 -1.665900 -1.482430
+
+# 165
+-0.684660 -0.477660 -0.348750 -0.462500 -0.271890
+-0.000430 0.196710 0.180860 -0.410680 -1.810120
+-2.675640 1.822690 -1.636020 -3.153350 -2.780320
+-1.715700 -0.534910 0.258100 0.329180 -0.126160
+-0.940260 -1.319240 -0.990850 -0.896700
+
+# glycine before proline map, type 6
+
+# -180
+-0.549160 -0.535500 -0.588110 -0.754620 -0.679290
+-0.038150 0.298460 0.326040 -0.375610 -1.704360
+-3.061280 -3.956460 -3.576280 -1.038930 2.012450
+-1.714610 -0.377660 0.317310 0.294580 -0.042920
+-0.676620 -0.744600 -0.586590 -0.554770
+
+# -165
+-0.709450 -0.896700 -0.990850 -1.319240 -0.940260
+-0.126160 0.329180 0.258100 -0.534910 -1.715700
+-2.780320 -3.153350 -1.636020 1.822690 -2.675640
+-1.810120 -0.410680 0.180860 0.196710 -0.000430
+-0.271890 -0.462500 -0.348750 -0.477660
+
+# -150
+-1.224850 -1.482430 -1.665900 -1.656770 -1.119780
+-1.642540 -0.054220 -0.290670 -0.887080 -1.626260
+-2.165440 -1.546500 0.753400 -2.949180 -2.225630
+-1.664160 -0.628990 0.000490 0.033160 -0.092820
+-0.339050 -0.563330 -0.794980 -0.710760
+
+# -135
+-1.787640 -2.117750 -2.143020 -1.803720 -1.567160
+-0.886880 -0.801350 -0.851590 -1.020630 -1.337360
+-1.062570 0.338010 -4.372310 -2.435890 -2.220710
+-1.718060 -0.758950 -0.207560 0.100910 -0.055650
+-0.288370 -0.880610 -1.267450 -1.465530
+
+# -120
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+-1.705860 -1.435540 -1.289220 -1.358170 -0.975570
+-3.514390 -4.283210 -3.975820 -3.215190 -2.394430
+-1.455320 -0.553910 -0.158900 -0.173830 -0.297950
+-0.661220 -1.068330 -1.601800 -1.914850
+
+# -105
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+-2.266680 -1.951490 -1.681850 -1.195390 -2.567680
+-3.632800 -4.748210 -4.662850 -4.255190 -2.776760
+-1.695490 -0.893140 -0.633810 -0.467320 -0.540540
+-0.950190 -1.401500 -1.959970 -2.412680
+
+# -90
+-3.857170 -3.713610 -3.902110 -3.611370 -3.040850
+-2.406460 -1.975250 -1.452040 -0.971860 -2.808170
+-4.181160 -4.981430 -5.446890 -4.359900 -2.864390
+-1.898510 -1.139090 -0.971340 -1.065550 -1.020680
+-1.141350 -1.794480 -2.420970 -2.939990
+
+# -75
+-4.987770 -4.995210 -4.485310 -3.892550 -3.228630
+-2.345360 -1.664160 -1.105500 -1.945510 -3.715530
+-4.492140 -5.536170 -5.708500 -3.675410 -2.986660
+-1.859410 -0.756620 -1.269930 -1.312730 -1.607440
+-1.892510 -2.659400 -3.347950 -3.970600
+
+# -60
+-6.183650 -5.456080 -4.878940 -4.000820 -2.683230
+-2.067520 -1.094850 -1.119790 -2.962910 -3.687830
+-4.993340 -4.666260 -3.796280 -3.374140 -2.495430
+-1.453990 -0.877560 -1.002930 -1.337310 -2.431360
+-2.948140 -4.008100 -4.821040 -5.565810
+
+# -45
+-6.755760 -5.850030 -4.362190 -2.714090 -1.708710
+-0.526660 -0.536700 -2.037170 -3.892650 -4.558570
+-4.237410 -3.735160 -3.688580 -3.009910 -2.112940
+-1.455400 -0.925490 -1.121840 -1.561900 -2.751370
+-4.094860 -5.207530 -6.128530 -6.613030
+
+# -30
+-5.716250 -4.434060 -2.788600 -0.974400 -0.729200
+-0.904940 -1.833540 -3.017700 -3.313450 -3.336010
+-3.181640 -3.594720 -1.231370 -0.603790 0.128810
+-1.222610 -0.909150 -0.837700 -1.346820 -3.040880
+-4.731110 -5.844860 -6.428460 -6.424880
+
+# -15
+-3.991110 -2.046000 0.082550 -2.676110 -2.828500
+-2.596640 -2.843330 -3.011480 -2.312640 -2.405980
+-3.086210 -1.164620 -1.231660 -0.871900 -0.348980
+-1.735900 -0.914150 -0.484520 -1.818040 -3.602550
+-5.330320 -5.992270 -5.588080 -5.408360
+
+# 0
+-1.147060 -3.317730 -4.305100 -4.615200 -4.533780
+-3.622950 -2.832800 -1.872810 -1.144300 -1.994070
+-0.741980 -1.115010 -1.229250 -1.103680 -0.742430
+-1.973970 -1.070020 -1.802220 -2.712770 -3.624130
+-4.537100 -4.619970 -4.310890 -3.318290
+
+# 15
+-3.997710 -5.408360 -5.588080 -5.992270 -5.330320
+-3.602550 -1.818040 -0.484520 -0.914150 -1.735900
+-0.348980 -0.871900 -1.231660 -1.164620 -3.086210
+-2.405980 -2.312640 -3.011480 -2.843330 -2.596640
+-2.828500 -2.676110 0.082550 -2.046000
+
+# 30
+-5.710850 -6.424880 -6.428460 -5.844860 -4.731110
+-3.040880 -1.346820 -0.837700 -0.909150 -1.222610
+0.128810 -0.603790 -1.231370 -3.594720 -3.181640
+-3.336010 -3.313450 -3.017700 -1.833540 -0.904940
+-0.729200 -0.974400 -2.788600 -4.434060
+
+# 45
+-6.754940 -6.613030 -6.128530 -5.207530 -4.094860
+-2.751370 -1.561900 -1.121840 -0.925490 -1.455400
+-2.112940 -3.009910 -3.688580 -3.735160 -4.237410
+-4.558570 -3.892650 -2.037170 -0.536700 -0.526660
+-1.708710 -2.714090 -4.362190 -5.850030
+
+# 60
+-6.188070 -5.565810 -4.821040 -4.008100 -2.948140
+-2.431360 -1.337310 -1.002930 -0.877560 -1.453990
+-2.495430 -3.374140 -3.796280 -4.666260 -4.993340
+-3.687830 -2.962910 -1.119790 -1.094850 -2.067520
+-2.683230 -4.000820 -4.878940 -5.456080
+
+# 75
+-4.986080 -3.970600 -3.347950 -2.659400 -1.892510
+-1.607440 -1.312730 -1.269930 -0.756620 -1.859410
+-2.986660 -3.675410 -5.708500 -5.536170 -4.492140
+-3.715530 -1.945510 -1.105500 -1.664160 -2.345360
+-3.228630 -3.892550 -4.485310 -4.995210
+
+# 90
+-3.879190 -2.939990 -2.420970 -1.794480 -1.141350
+-1.020680 -1.065550 -0.971340 -1.139090 -1.898510
+-2.864390 -4.359900 -5.446890 -4.981430 -4.181160
+-2.808170 -0.971860 -1.452040 -1.975250 -2.406460
+-3.040850 -3.611370 -3.902110 -3.713610
+
+# 105
+-2.793280 -2.412680 -1.959970 -1.401500 -0.950190
+-0.540540 -0.467320 -0.633810 -0.893140 -1.695490
+-2.776760 -4.255190 -4.662850 -4.448210 -3.332800
+-2.567680 -1.195390 -1.681850 -1.951490 -2.266680
+-2.626630 -3.013710 -3.178150 -3.079570
+
+# 120
+-2.330190 -1.914850 -1.601800 -1.068330 -0.661220
+-0.297950 -0.173830 -0.158900 -0.553910 -1.455320
+-2.394430 -3.215190 -3.975820 -3.783210 -3.014390
+-0.975570 -1.358170 -1.289220 -1.435540 -1.705860
+-1.970070 -2.364070 -2.596140 -2.593790
+
+# 135
+-1.796120 -1.465530 -1.267450 -0.880610 -0.288370
+-0.055650 0.100910 -0.207560 -0.758950 -1.718060
+-2.220710 -2.435890 -4.372310 0.338010 -1.062570
+-1.337360 -1.020630 -0.851590 -0.801350 -0.886880
+-1.567160 -1.803720 -2.143020 -2.117750
+
+# 150
+-1.263610 -0.710760 -0.794980 -0.563330 -0.339050
+-0.092820 0.033160 0.000490 -0.628990 -1.664160
+-2.225630 -2.949180 0.753400 -1.546500 -2.165440
+-1.626260 -0.887080 -0.290670 -0.054220 -1.642540
+-1.119780 -1.656770 -1.665900 -1.482430
+
+# 165
+-0.684660 -0.477660 -0.348750 -0.462500 -0.271890
+-0.000430 0.196710 0.180860 -0.410680 -1.810120
+-2.675640 1.822690 -1.636020 -3.153350 -2.780320
+-1.715700 -0.534910 0.258100 0.329180 -0.126160
+-0.940260 -1.319240 -0.990850 -0.896700
+
diff --git a/examples/cmap/gagg.data b/examples/cmap/gagg.data
new file mode 100644
index 0000000000000000000000000000000000000000..fd2aa193c4450f998cc7e265621cb1688c967eb7
--- /dev/null
+++ b/examples/cmap/gagg.data
@@ -0,0 +1,380 @@
+Created by charmm2lammps v1.8.2.6 beta on Sun Mar 20 00:26:35 EDT 2016
+
+ 34 atoms
+ 33 bonds
+ 57 angles
+ 75 dihedrals
+ 7 impropers
+ 2 crossterms
+
+ 13 atom types
+ 15 bond types
+ 30 angle types
+ 42 dihedral types
+ 5 improper types
+
+ -34.414709 45.585291 xlo xhi
+ -36.134827 43.865173 ylo yhi
+ -39.349142 40.650858 zlo zhi
+
+Masses
+
+ 1 1.008 # H
+ 2 1.008 # HC
+ 3 1.008 # HA
+ 4 1.008 # HB
+ 5 12.011 # C
+ 6 12.011 # CT1
+ 7 12.011 # CT2
+ 8 12.011 # CT3
+ 9 12.011 # CC
+ 10 14.007 # NH1
+ 11 14.007 # NH3
+ 12 15.999 # O
+ 13 15.999 # OC
+
+Pair Coeffs
+
+ 1 0.046 0.400013524445 0.046 0.400013524445 # H
+ 2 0.046 0.400013524445 0.046 0.400013524445 # HC
+ 3 0.022 2.35197261589 0.022 2.35197261589 # HA
+ 4 0.022 2.35197261589 0.022 2.35197261589 # HB
+ 5 0.11 3.56359487256 0.11 3.56359487256 # C
+ 6 0.02 4.05358916754 0.01 3.38541512893 # CT1
+ 7 0.055 3.87540942391 0.01 3.38541512893 # CT2
+ 8 0.08 3.67050271874 0.01 3.38541512893 # CT3
+ 9 0.07 3.56359487256 0.07 3.56359487256 # CC
+ 10 0.2 3.29632525712 0.2 2.76178602624 # NH1
+ 11 0.2 3.29632525712 0.2 3.29632525712 # NH3
+ 12 0.12 3.02905564168 0.12 2.49451641079 # O
+ 13 0.12 3.02905564168 0.12 3.02905564168 # OC
+
+Atoms
+
+ 1 1 11 -0.3 0.0088076654 -0.0395361015 -0.0125765907 # NH3
+ 2 1 2 0.33 -0.3781208354 -1.0038773849 -0.01724272 # HC
+ 3 1 2 0.33 -0.3448285543 0.4901827566 -0.8403800387 # HC
+ 4 1 2 0.33 -0.3306420078 0.4732826156 0.8294424358 # HC
+ 5 1 7 0.13 1.526230489 -0.0164860529 -0.0402820599 # CT2
+ 6 1 4 0.09 1.8596639218 -0.5263587482 -0.9333647137 # HB
+ 7 1 4 0.09 1.8904342902 -0.4510777655 0.8809945249 # HB
+ 8 1 5 0.51 2.0135471936 1.4020233344 -0.1137107587 # C
+ 9 1 12 -0.51 1.1818164992 2.2781068718 -0.313197467 # O
+ 10 2 10 -0.47 3.3194424268 1.666672014 0.0713249543 # NH1
+ 11 2 1 0.31 4.0409429153 0.9783582555 0.1693897169 # H
+ 12 2 6 0.07 3.8529467728 3.0161771739 0.0690818527 # CT1
+ 13 2 4 0.09 3.5315723829 3.5134434764 -0.8378950509 # HB
+ 14 2 8 -0.27 3.3981217437 3.8178727883 1.3071600161 # CT3
+ 15 2 3 0.09 2.2921877645 3.9163330652 1.3111957959 # HA
+ 16 2 3 0.09 3.7142964083 3.3104118688 2.2424399743 # HA
+ 17 2 3 0.09 3.8238672849 4.8446179852 1.2978564897 # HA
+ 18 2 5 0.51 5.3731873136 2.946062408 0.0042414688 # C
+ 19 2 12 -0.51 5.9268816775 1.8488403755 0.0011766847 # O
+ 20 3 10 -0.47 6.0445386951 4.1111769168 -0.0636349698 # NH1
+ 21 3 1 0.31 5.5768514013 4.9972489389 -0.0653583036 # H
+ 22 3 7 -0.02 7.4911642129 4.2772062416 -0.0346088891 # CT2
+ 23 3 4 0.09 7.9218377956 3.8786283786 -0.9407244447 # HB
+ 24 3 4 0.09 7.8877470687 3.8607990619 0.8803359097 # HB
+ 25 3 5 0.51 7.7351287723 5.7597169026 -0.0088736611 # C
+ 26 3 12 -0.51 6.7657462979 6.5189223559 0.005150418 # O
+ 27 4 10 -0.47 9.0014031015 6.1940849758 -0.0045995102 # NH1
+ 28 4 1 0.31 9.8272711181 5.6225413025 -0.008448093 # H
+ 29 4 7 -0.02 9.4067557288 7.5845263022 0.0016383819 # CT2
+ 30 4 4 0.09 9.0736276253 8.0578903151 0.9119901724 # HB
+ 31 4 4 0.09 9.0736165596 8.064051906 -0.9055419386 # HB
+ 32 4 9 0.34 10.9382207556 7.612479283 0.0008762597 # CC
+ 33 4 13 -0.67 11.5487033003 6.5062943609 -0.0007524693 # OC
+ 34 4 13 -0.67 11.5055524841 8.734223435 0.0013684148 # OC
+
+Bond Coeffs
+
+ 1 250 1.49 # C CT1
+ 2 250 1.49 # C CT2
+ 3 370 1.345 # C NH1
+ 4 620 1.23 # C O
+ 5 200 1.522 # CC CT2
+ 6 525 1.26 # CC OC
+ 7 222.5 1.538 # CT1 CT3
+ 8 330 1.08 # CT1 HB
+ 9 320 1.43 # CT1 NH1
+ 10 330 1.08 # CT2 HB
+ 11 320 1.43 # CT2 NH1
+ 12 200 1.48 # CT2 NH3
+ 13 322 1.111 # CT3 HA
+ 14 440 0.997 # H NH1
+ 15 403 1.04 # HC NH3
+
+Bonds
+
+ 1 15 2 1 # HC NH3
+ 2 15 3 1 # HC NH3
+ 3 15 4 1 # HC NH3
+ 4 12 1 5 # CT2 NH3
+ 5 2 8 5 # C CT2
+ 6 3 8 10 # C NH1
+ 7 10 5 6 # CT2 HB
+ 8 10 5 7 # CT2 HB
+ 9 4 9 8 # C O
+ 10 7 14 12 # CT1 CT3
+ 11 14 10 11 # H NH1
+ 12 9 10 12 # CT1 NH1
+ 13 1 18 12 # C CT1
+ 14 3 18 20 # C NH1
+ 15 8 12 13 # CT1 HB
+ 16 13 14 15 # CT3 HA
+ 17 13 14 16 # CT3 HA
+ 18 13 14 17 # CT3 HA
+ 19 4 19 18 # C O
+ 20 14 20 21 # H NH1
+ 21 11 20 22 # CT2 NH1
+ 22 2 25 22 # C CT2
+ 23 3 25 27 # C NH1
+ 24 10 22 23 # CT2 HB
+ 25 10 22 24 # CT2 HB
+ 26 4 26 25 # C O
+ 27 14 27 28 # H NH1
+ 28 11 27 29 # CT2 NH1
+ 29 5 32 29 # CC CT2
+ 30 10 29 30 # CT2 HB
+ 31 10 29 31 # CT2 HB
+ 32 6 32 34 # CC OC
+ 33 6 32 33 # CC OC
+
+Angle Coeffs
+
+ 1 52 108 0 0 # C CT1 CT3
+ 2 50 109.5 0 0 # C CT1 HB
+ 3 50 107 0 0 # C CT1 NH1
+ 4 50 109.5 0 0 # C CT2 HB
+ 5 50 107 0 0 # C CT2 NH1
+ 6 43.7 110 0 0 # C CT2 NH3
+ 7 50 120 0 0 # C NH1 CT1
+ 8 50 120 0 0 # C NH1 CT2
+ 9 34 123 0 0 # C NH1 H
+ 10 50 109.5 0 0 # CC CT2 HB
+ 11 50 107 0 0 # CC CT2 NH1
+ 12 80 116.5 0 0 # CT1 C NH1
+ 13 80 121 0 0 # CT1 C O
+ 14 33.43 110.1 22.53 2.179 # CT1 CT3 HA
+ 15 35 117 0 0 # CT1 NH1 H
+ 16 80 116.5 0 0 # CT2 C NH1
+ 17 80 121 0 0 # CT2 C O
+ 18 40 118 50 2.388 # CT2 CC OC
+ 19 35 117 0 0 # CT2 NH1 H
+ 20 30 109.5 20 2.074 # CT2 NH3 HC
+ 21 35 111 0 0 # CT3 CT1 HB
+ 22 70 113.5 0 0 # CT3 CT1 NH1
+ 23 35.5 108.4 5.4 1.802 # HA CT3 HA
+ 24 48 108 0 0 # HB CT1 NH1
+ 25 36 115 0 0 # HB CT2 HB
+ 26 48 108 0 0 # HB CT2 NH1
+ 27 51.5 107.5 0 0 # HB CT2 NH3
+ 28 44 109.5 0 0 # HC NH3 HC
+ 29 80 122.5 0 0 # NH1 C O
+ 30 100 124 70 2.225 # OC CC OC
+
+Angles
+
+ 1 28 2 1 3 # HC NH3 HC
+ 2 28 2 1 4 # HC NH3 HC
+ 3 20 2 1 5 # CT2 NH3 HC
+ 4 28 3 1 4 # HC NH3 HC
+ 5 20 3 1 5 # CT2 NH3 HC
+ 6 20 4 1 5 # CT2 NH3 HC
+ 7 27 1 5 6 # HB CT2 NH3
+ 8 27 1 5 7 # HB CT2 NH3
+ 9 6 1 5 8 # C CT2 NH3
+ 10 25 6 5 7 # HB CT2 HB
+ 11 4 6 5 8 # C CT2 HB
+ 12 4 7 5 8 # C CT2 HB
+ 13 17 5 8 9 # CT2 C O
+ 14 16 5 8 10 # CT2 C NH1
+ 15 29 9 8 10 # NH1 C O
+ 16 9 8 10 11 # C NH1 H
+ 17 7 8 10 12 # C NH1 CT1
+ 18 15 11 10 12 # CT1 NH1 H
+ 19 24 10 12 13 # HB CT1 NH1
+ 20 22 10 12 14 # CT3 CT1 NH1
+ 21 3 10 12 18 # C CT1 NH1
+ 22 21 13 12 14 # CT3 CT1 HB
+ 23 2 13 12 18 # C CT1 HB
+ 24 1 14 12 18 # C CT1 CT3
+ 25 14 12 14 15 # CT1 CT3 HA
+ 26 14 12 14 16 # CT1 CT3 HA
+ 27 14 12 14 17 # CT1 CT3 HA
+ 28 23 15 14 16 # HA CT3 HA
+ 29 23 15 14 17 # HA CT3 HA
+ 30 23 16 14 17 # HA CT3 HA
+ 31 13 12 18 19 # CT1 C O
+ 32 12 12 18 20 # CT1 C NH1
+ 33 29 19 18 20 # NH1 C O
+ 34 9 18 20 21 # C NH1 H
+ 35 8 18 20 22 # C NH1 CT2
+ 36 19 21 20 22 # CT2 NH1 H
+ 37 26 20 22 23 # HB CT2 NH1
+ 38 26 20 22 24 # HB CT2 NH1
+ 39 5 20 22 25 # C CT2 NH1
+ 40 25 23 22 24 # HB CT2 HB
+ 41 4 23 22 25 # C CT2 HB
+ 42 4 24 22 25 # C CT2 HB
+ 43 17 22 25 26 # CT2 C O
+ 44 16 22 25 27 # CT2 C NH1
+ 45 29 26 25 27 # NH1 C O
+ 46 9 25 27 28 # C NH1 H
+ 47 8 25 27 29 # C NH1 CT2
+ 48 19 28 27 29 # CT2 NH1 H
+ 49 26 27 29 30 # HB CT2 NH1
+ 50 26 27 29 31 # HB CT2 NH1
+ 51 11 27 29 32 # CC CT2 NH1
+ 52 25 30 29 31 # HB CT2 HB
+ 53 10 30 29 32 # CC CT2 HB
+ 54 10 31 29 32 # CC CT2 HB
+ 55 18 29 32 33 # CT2 CC OC
+ 56 18 29 32 34 # CT2 CC OC
+ 57 30 33 32 34 # OC CC OC
+
+Dihedral Coeffs
+
+ 1 0.2 3 0 1 # C CT1 CT3 HA
+ 2 0.2 1 180 1 # C CT1 NH1 C
+ 3 0 1 0 1 # C CT1 NH1 H
+ 4 0.2 1 180 1 # C CT2 NH1 C
+ 5 0 1 0 1 # C CT2 NH1 H
+ 6 0.1 3 0 1 # C CT2 NH3 HC
+ 7 1.8 1 0 1 # C NH1 CT1 CT3
+ 8 0 1 0 1 # C NH1 CT1 HB
+ 9 0.2 1 180 1 # C NH1 CT2 CC
+ 10 0 1 0 1 # C NH1 CT2 HB
+ 11 0 1 0 1 # CC CT2 NH1 H
+ 12 1.6 1 0 1 # CT1 C NH1 CT2
+ 13 2.5 2 180 0 # CT1 C NH1 CT2
+ 14 2.5 2 180 1 # CT1 C NH1 H
+ 15 1.6 1 0 1 # CT1 NH1 C CT2
+ 16 2.5 2 180 0 # CT1 NH1 C CT2
+ 17 2.5 2 180 1 # CT1 NH1 C O
+ 18 1.6 1 0 1 # CT2 C NH1 CT2
+ 19 2.5 2 180 0 # CT2 C NH1 CT2
+ 20 2.5 2 180 1 # CT2 C NH1 H
+ 21 2.5 2 180 1 # CT2 NH1 C O
+ 22 0 1 0 1 # CT3 CT1 C NH1
+ 23 1.4 1 0 1 # CT3 CT1 C O
+ 24 0 1 0 1 # CT3 CT1 NH1 H
+ 25 2.5 2 180 1 # H NH1 C O
+ 26 0 1 0 1 # H NH1 CT1 HB
+ 27 0 1 0 1 # H NH1 CT2 HB
+ 28 0.2 3 0 1 # HA CT3 CT1 HB
+ 29 0.2 3 0 1 # HA CT3 CT1 NH1
+ 30 0 1 0 1 # HB CT1 C NH1
+ 31 0 1 0 1 # HB CT1 C O
+ 32 0 1 0 1 # HB CT2 C NH1
+ 33 0 1 0 1 # HB CT2 C O
+ 34 0.05 6 180 1 # HB CT2 CC OC
+ 35 0.1 3 0 1 # HB CT2 NH3 HC
+ 36 0.6 1 0 1 # NH1 C CT1 NH1
+ 37 0.6 1 0 1 # NH1 C CT2 NH1
+ 38 0.4 1 0 1 # NH1 C CT2 NH3
+ 39 0 1 0 1 # NH1 CT1 C O
+ 40 0 1 0 1 # NH1 CT2 C O
+ 41 0.05 6 180 1 # NH1 CT2 CC OC
+ 42 0 1 0 1 # NH3 CT2 C O
+
+Dihedrals
+
+ 1 42 1 5 8 9 # NH3 CT2 C O
+ 2 38 1 5 8 10 # NH1 C CT2 NH3
+ 3 35 2 1 5 6 # HB CT2 NH3 HC
+ 4 35 2 1 5 7 # HB CT2 NH3 HC
+ 5 6 2 1 5 8 # C CT2 NH3 HC
+ 6 35 3 1 5 6 # HB CT2 NH3 HC
+ 7 35 3 1 5 7 # HB CT2 NH3 HC
+ 8 6 3 1 5 8 # C CT2 NH3 HC
+ 9 35 4 1 5 6 # HB CT2 NH3 HC
+ 10 35 4 1 5 7 # HB CT2 NH3 HC
+ 11 6 4 1 5 8 # C CT2 NH3 HC
+ 12 20 5 8 10 11 # CT2 C NH1 H
+ 13 15 5 8 10 12 # CT1 NH1 C CT2
+ 14 16 5 8 10 12 # CT1 NH1 C CT2
+ 15 33 6 5 8 9 # HB CT2 C O
+ 16 32 6 5 8 10 # HB CT2 C NH1
+ 17 33 7 5 8 9 # HB CT2 C O
+ 18 32 7 5 8 10 # HB CT2 C NH1
+ 19 8 8 10 12 13 # C NH1 CT1 HB
+ 20 7 8 10 12 14 # C NH1 CT1 CT3
+ 21 2 8 10 12 18 # C CT1 NH1 C
+ 22 25 9 8 10 11 # H NH1 C O
+ 23 17 9 8 10 12 # CT1 NH1 C O
+ 24 29 10 12 14 15 # HA CT3 CT1 NH1
+ 25 29 10 12 14 16 # HA CT3 CT1 NH1
+ 26 29 10 12 14 17 # HA CT3 CT1 NH1
+ 27 39 10 12 18 19 # NH1 CT1 C O
+ 28 36 10 12 18 20 # NH1 C CT1 NH1
+ 29 26 11 10 12 13 # H NH1 CT1 HB
+ 30 24 11 10 12 14 # CT3 CT1 NH1 H
+ 31 3 11 10 12 18 # C CT1 NH1 H
+ 32 14 12 18 20 21 # CT1 C NH1 H
+ 33 12 12 18 20 22 # CT1 C NH1 CT2
+ 34 13 12 18 20 22 # CT1 C NH1 CT2
+ 35 28 13 12 14 15 # HA CT3 CT1 HB
+ 36 28 13 12 14 16 # HA CT3 CT1 HB
+ 37 28 13 12 14 17 # HA CT3 CT1 HB
+ 38 31 13 12 18 19 # HB CT1 C O
+ 39 30 13 12 18 20 # HB CT1 C NH1
+ 40 23 14 12 18 19 # CT3 CT1 C O
+ 41 22 14 12 18 20 # CT3 CT1 C NH1
+ 42 1 15 14 12 18 # C CT1 CT3 HA
+ 43 1 16 14 12 18 # C CT1 CT3 HA
+ 44 1 17 14 12 18 # C CT1 CT3 HA
+ 45 10 18 20 22 23 # C NH1 CT2 HB
+ 46 10 18 20 22 24 # C NH1 CT2 HB
+ 47 4 18 20 22 25 # C CT2 NH1 C
+ 48 25 19 18 20 21 # H NH1 C O
+ 49 21 19 18 20 22 # CT2 NH1 C O
+ 50 40 20 22 25 26 # NH1 CT2 C O
+ 51 37 20 22 25 27 # NH1 C CT2 NH1
+ 52 27 21 20 22 23 # H NH1 CT2 HB
+ 53 27 21 20 22 24 # H NH1 CT2 HB
+ 54 5 21 20 22 25 # C CT2 NH1 H
+ 55 20 22 25 27 28 # CT2 C NH1 H
+ 56 18 22 25 27 29 # CT2 C NH1 CT2
+ 57 19 22 25 27 29 # CT2 C NH1 CT2
+ 58 33 23 22 25 26 # HB CT2 C O
+ 59 32 23 22 25 27 # HB CT2 C NH1
+ 60 33 24 22 25 26 # HB CT2 C O
+ 61 32 24 22 25 27 # HB CT2 C NH1
+ 62 10 25 27 29 30 # C NH1 CT2 HB
+ 63 10 25 27 29 31 # C NH1 CT2 HB
+ 64 9 25 27 29 32 # C NH1 CT2 CC
+ 65 25 26 25 27 28 # H NH1 C O
+ 66 21 26 25 27 29 # CT2 NH1 C O
+ 67 41 27 29 32 33 # NH1 CT2 CC OC
+ 68 41 27 29 32 34 # NH1 CT2 CC OC
+ 69 27 28 27 29 30 # H NH1 CT2 HB
+ 70 27 28 27 29 31 # H NH1 CT2 HB
+ 71 11 28 27 29 32 # CC CT2 NH1 H
+ 72 34 30 29 32 33 # HB CT2 CC OC
+ 73 34 30 29 32 34 # HB CT2 CC OC
+ 74 34 31 29 32 33 # HB CT2 CC OC
+ 75 34 31 29 32 34 # HB CT2 CC OC
+
+Improper Coeffs
+
+ 1 120 0 # C CT1 NH1 O
+ 2 120 0 # C CT2 NH1 O
+ 3 96 0 # CC CT2 OC OC
+ 4 20 0 # H CT1 C NH1
+ 5 20 0 # H CT2 C NH1
+
+Impropers
+
+ 1 2 8 5 10 9 # C CT2 NH1 O
+ 2 4 10 8 12 11 # H CT1 C NH1
+ 3 1 18 12 20 19 # C CT1 NH1 O
+ 4 5 20 18 22 21 # H CT2 C NH1
+ 5 2 25 22 27 26 # C CT2 NH1 O
+ 6 5 27 25 29 28 # H CT2 C NH1
+ 7 3 32 29 34 33 # CC CT2 OC OC
+
+CMAP
+
+ 1 1 8 10 12 18 20
+ 2 5 18 20 22 25 27
diff --git a/examples/cmap/in.cmap b/examples/cmap/in.cmap
new file mode 100644
index 0000000000000000000000000000000000000000..d2b2714b826fc2f25abc00b2ec0c265726dc3e87
--- /dev/null
+++ b/examples/cmap/in.cmap
@@ -0,0 +1,36 @@
+# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016
+
+units real
+neigh_modify delay 2 every 1
+#newton off
+
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style charmm
+dihedral_style charmm
+improper_style harmonic
+
+pair_style lj/charmm/coul/charmm 8 12
+#pair_style lj/charmmfsw/coul/charmmfsh 8 12
+pair_modify mix arithmetic
+
+fix cmap all cmap charmm22.cmap
+fix_modify cmap energy yes
+
+read_data gagg.data fix cmap crossterm CMAP
+
+special_bonds charmm
+fix 1 all nve
+
+#fix 1 all nvt temp 300 300 100.0
+#fix 2 all shake 1e-9 500 0 m 1.0
+
+velocity all create 0.0 12345678 dist uniform
+
+thermo 1000
+thermo_style custom step ecoul evdwl ebond eangle edihed f_cmap eimp
+timestep 2.0
+
+run 100000
diff --git a/examples/cmap/log.23Sep16.cmap.g++.1 b/examples/cmap/log.23Sep16.cmap.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..fe6caed913654df89fda147406a032e217fab0b1
--- /dev/null
+++ b/examples/cmap/log.23Sep16.cmap.g++.1
@@ -0,0 +1,200 @@
+LAMMPS (21 Sep 2016)
+# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016
+
+units real
+neigh_modify delay 2 every 1
+#newton off
+
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style charmm
+dihedral_style charmm
+improper_style harmonic
+
+pair_style lj/charmm/coul/charmm 8 12
+#pair_style lj/charmmfsw/coul/charmmfsh 8 12
+pair_modify mix arithmetic
+
+fix cmap all cmap charmm22.cmap
+fix_modify cmap energy yes
+
+read_data gagg.data fix cmap crossterm CMAP
+ orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 34 atoms
+ scanning bonds ...
+ 4 = max bonds/atom
+ scanning angles ...
+ 6 = max angles/atom
+ scanning dihedrals ...
+ 12 = max dihedrals/atom
+ scanning impropers ...
+ 1 = max impropers/atom
+ reading bonds ...
+ 33 bonds
+ reading angles ...
+ 57 angles
+ reading dihedrals ...
+ 75 dihedrals
+ reading impropers ...
+ 7 impropers
+ 4 = max # of 1-2 neighbors
+ 7 = max # of 1-3 neighbors
+ 13 = max # of 1-4 neighbors
+ 16 = max # of special neighbors
+
+special_bonds charmm
+fix 1 all nve
+
+#fix 1 all nvt temp 300 300 100.0
+#fix 2 all shake 1e-9 500 0 m 1.0
+
+velocity all create 0.0 12345678 dist uniform
+
+thermo 1000
+thermo_style custom step ecoul evdwl ebond eangle edihed f_cmap eimp
+timestep 2.0
+
+run 100000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 2 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 14
+ ghost atom cutoff = 14
+ binsize = 7 -> bins = 12 12 12
+Memory usage per processor = 14.6355 Mbytes
+Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro
+ 0 26.542777 -0.93822087 1.2470497 4.8441789 4.5432816 -1.473352 0.10453023
+ 1000 28.673005 -0.47724367 0.80029132 3.151679 4.4684446 -2.3928648 0.18604953
+ 2000 27.67955 -1.170342 0.72018905 4.0400131 4.4713764 -2.5490207 0.21834436
+ 3000 29.256656 -0.35856055 0.73303546 3.7411606 4.4710568 -2.8939692 0.37728884
+ 4000 30.097549 -1.1353905 0.79007053 3.0688444 4.4091469 -2.3383587 0.20743631
+ 5000 28.357525 -1.0723742 0.9180297 3.6579424 4.8792664 -2.3185572 0.088366962
+ 6000 29.214175 -0.95299225 0.81926009 3.6805429 4.6742897 -2.9343577 0.26697813
+ 7000 27.018614 -0.52423475 0.72502764 3.8840137 4.7780956 -2.3916009 0.24952584
+ 8000 29.682167 -1.0939711 0.76111486 3.1090116 4.9359719 -2.5662984 0.1411154
+ 9000 27.909695 -0.80905986 0.78952533 4.203187 4.1301204 -2.000402 0.088859259
+ 10000 27.480298 -0.86273377 1.1293962 4.3857421 4.899282 -3.3895621 0.12126215
+ 11000 28.303203 -1.0221152 0.62762348 4.055414 4.5863024 -2.5842816 0.17996907
+ 12000 28.311127 -0.94227367 0.91859012 3.6673926 4.7018632 -3.902715 0.30065704
+ 13000 30.818607 -1.5220116 0.95710386 3.3364371 4.543427 -3.0423067 0.16712905
+ 14000 27.643736 -1.0144117 0.95806952 4.1046912 4.800236 -4.0534389 0.29293405
+ 15000 27.660491 -1.0390086 0.78061056 4.1139174 4.7197202 -2.3670379 0.22126985
+ 16000 27.845157 -0.63654502 0.78007478 3.9365994 4.949418 -3.1470214 0.22335355
+ 17000 28.44772 -1.0255112 0.70402007 4.0573343 4.2887527 -2.2099596 0.048050962
+ 18000 27.128323 -0.96218536 1.1327159 4.3222585 4.326607 -2.2881766 0.13491257
+ 19000 27.337633 -0.78999574 0.80152298 4.2239689 4.7073478 -2.2924164 0.12710292
+ 20000 27.780537 -0.46458072 0.79707671 3.7232618 4.943417 -2.5290628 0.26191223
+ 21000 26.435484 -0.7803224 1.0753217 4.4196051 5.9945933 -2.3340925 0.16448475
+ 22000 28.619429 -1.1623149 0.9401731 3.8508844 5.1636737 -2.5551846 0.25318434
+ 23000 28.399338 -0.79700962 0.85575503 4.488526 4.5975422 -2.5663549 0.13601693
+ 24000 29.645532 -1.158744 0.83180313 3.8193399 4.60319 -2.6847864 0.24260466
+ 25000 28.695339 -1.4802204 0.76583757 3.6786272 4.8959496 -2.3627896 0.080867326
+ 26000 28.149711 -1.029689 0.79383806 3.7885067 4.3345813 -2.1041553 0.14598209
+ 27000 29.580373 -1.0525813 1.0262723 3.7767318 4.6119758 -2.2802386 0.088556038
+ 28000 28.44308 -0.93411225 0.8794395 3.948079 4.780246 -2.1814583 0.14340149
+ 29000 29.335621 -1.6087988 0.71803091 3.7819186 4.6688385 -2.4282242 0.16061111
+ 30000 28.706138 -1.3938241 0.67713818 4.031275 4.4756505 -2.1807056 0.11461356
+ 31000 27.451944 0.010297225 0.65064883 3.6402029 4.3607811 -2.5511516 0.12637237
+ 32000 27.070878 -1.103158 1.1932199 5.1329709 4.5201653 -2.2224479 0.11215427
+ 33000 29.889976 -1.6228316 0.69407996 3.5361991 4.3502767 -1.9847454 0.09089949
+ 34000 28.223151 -0.927208 1.043253 3.4650939 5.1028142 -2.8127219 0.10648823
+ 35000 27.985986 -0.48153861 0.63878449 3.3724641 4.9551679 -2.6565919 0.12123115
+ 36000 28.580688 -1.4500694 1.055762 4.0490064 4.423782 -2.3103578 0.072747638
+ 37000 29.192947 -0.49678176 1.1146731 2.9233947 4.5738603 -2.4376144 0.22874047
+ 38000 26.954594 -0.53812359 0.79230685 4.3356989 5.0284656 -2.3791255 0.0486081
+ 39000 27.567555 -0.57870028 0.73614374 4.191991 4.9209556 -2.6122044 0.08635571
+ 40000 28.494172 -0.79057135 0.79072816 4.1893209 4.4826919 -2.4179635 0.14612898
+ 41000 28.44904 -1.1002948 0.93405654 4.3586358 4.4338415 -2.2950944 0.15705834
+ 42000 28.95725 -1.0297067 1.1632348 4.274711 4.9979487 -2.7611464 0.15944725
+ 43000 28.640394 -0.70938882 0.68100893 3.1844315 5.1817454 -2.2837487 0.14189233
+ 44000 27.997558 -1.0115099 0.59125208 4.0883422 4.6033907 -2.2775964 0.094273258
+ 45000 27.67163 -0.67992747 1.1225552 3.9020703 4.8171056 -2.1952679 0.041418433
+ 46000 28.822607 -0.6687953 0.74160059 3.3193715 4.5546965 -2.3024572 0.047569065
+ 47000 29.20147 -1.4456785 0.79223353 3.8288813 4.5811826 -2.5154936 0.061230141
+ 48000 27.843026 -1.0222301 0.87322137 4.3432743 4.4266307 -2.1414153 0.06802794
+ 49000 28.199573 -1.1887794 1.2781088 4.0779644 4.5881353 -2.319775 0.094803547
+ 50000 28.759212 -1.354416 0.68534569 3.8394841 4.2308134 -2.1281844 0.1395951
+ 51000 27.876455 -1.5705462 0.76557156 4.5335223 4.523708 -2.203702 0.14679803
+ 52000 27.930587 -1.2277489 0.96071516 3.960953 5.1152188 -2.4101451 0.060949521
+ 53000 27.031236 -1.4746477 1.2341141 5.0540975 4.3656865 -2.1288513 0.092725656
+ 54000 28.809394 -1.1162427 0.94350207 3.4013958 4.4755547 -2.3342811 0.18855912
+ 55000 28.948415 -1.1560418 0.6260139 3.5386373 4.5244978 -2.340212 0.17474657
+ 56000 28.048368 -0.95784532 0.76432571 4.1404665 4.4570033 -2.0899628 0.045693628
+ 57000 28.707642 -1.366574 0.9907873 3.729903 4.3131997 -2.2777698 0.065420213
+ 58000 26.361663 -1.0424403 1.0452563 5.0977108 4.7035231 -2.3101244 0.13671642
+ 59000 29.218218 -1.2210564 0.62435875 3.4236327 4.5481681 -2.1575943 0.037984042
+ 60000 27.655546 -1.1053224 0.86323501 3.7641375 4.8946898 -2.2422249 0.077725979
+ 61000 27.252108 -1.3744824 1.1150806 5.0444848 4.4878135 -2.2743829 0.058331257
+ 62000 27.163469 -1.1715781 0.72099321 4.5295501 4.9509918 -2.2993961 0.050401105
+ 63000 29.581575 -1.2238537 0.86303245 3.1194038 5.2218965 -2.5002427 0.055032632
+ 64000 27.897822 -1.1011516 0.74540883 4.2869228 4.3394269 -2.2552393 0.1403321
+ 65000 27.083245 -1.0633392 0.92771724 5.0805224 4.2747962 -2.2388039 0.064196692
+ 66000 29.072723 -1.5514209 0.89798805 4.2600224 4.4261812 -2.3524752 0.15067414
+ 67000 27.308181 -0.72224802 0.97109517 4.5074578 4.4559352 -2.1381121 0.089297603
+ 68000 27.505686 -0.43855431 0.80785812 4.1917251 5.0157721 -2.3382145 0.11105164
+ 69000 29.041681 -0.64735378 0.89874684 3.3891579 4.3753361 -2.2320941 0.14716747
+ 70000 29.735756 -1.7061457 0.9206878 3.5767878 4.3851664 -2.2516304 0.097196062
+ 71000 28.224352 -0.92217702 0.86093586 3.9507157 4.5596589 -2.2173397 0.089116669
+ 72000 29.282336 -1.056142 0.65185725 3.8735742 4.4839333 -2.4314756 0.071909704
+ 73000 26.257283 -0.64273826 0.98300685 5.063943 5.045958 -2.5544375 0.2180275
+ 74000 28.825119 -0.97736616 0.87201848 3.55875 4.3653309 -2.2303567 0.098963875
+ 75000 29.239507 -0.96508809 0.74517323 3.4306236 4.7651921 -2.6077732 0.17883654
+ 76000 27.349841 -0.50990238 1.1183613 4.4252451 4.4097775 -2.4125794 0.18483606
+ 77000 28.130197 -1.4081219 0.94921357 4.2572132 4.5162849 -2.4013797 0.073744606
+ 78000 28.235774 -0.9214321 0.6324981 3.8697686 4.8092154 -2.2272847 0.092108346
+ 79000 26.732846 -0.55949486 1.0989617 5.0088609 4.4930687 -2.277945 0.03855146
+ 80000 28.529208 -0.94244671 0.79407482 3.961106 4.3930011 -2.3127726 0.091124948
+ 81000 29.603852 -1.6116062 1.060847 3.7824932 4.151001 -1.9139868 0.19875986
+ 82000 28.232876 -1.1833011 1.0182713 3.4195758 5.1394333 -2.4632697 0.28501012
+ 83000 29.565482 -1.3479552 0.99056973 3.7851802 4.4781011 -2.7872481 0.2031991
+ 84000 28.780274 -1.3073882 1.0512637 4.004638 4.502282 -2.3789146 0.015656202
+ 85000 27.262312 -1.1305346 1.203524 4.7938623 4.1747105 -2.0952844 0.054240361
+ 86000 28.157348 -1.0662817 0.81163796 3.9912709 4.8320213 -2.255237 0.14698333
+ 87000 28.445543 -1.3365026 0.78156195 4.4767689 4.4457575 -2.5008786 0.13879386
+ 88000 27.656717 -1.1490599 0.87974869 4.4629952 4.7023033 -2.3258145 0.081904139
+ 89000 28.838821 -1.020709 0.85587929 3.7110705 4.4938307 -2.4914483 0.11447952
+ 90000 27.356497 -0.59107077 0.81879666 4.5209332 4.4703836 -2.3806717 0.071307775
+ 91000 27.780445 -0.80564513 0.94752313 3.8468943 4.2924253 -2.1011134 0.1118672
+ 92000 28.555276 -1.3514732 0.80826674 3.9590742 4.5775954 -2.4891232 0.054254978
+ 93000 28.747267 -1.2133243 0.75507246 4.1319789 4.9048611 -2.4913887 0.13045693
+ 94000 27.479343 -0.69973695 0.99696121 3.5966229 4.549025 -2.4155312 0.41745762
+ 95000 27.726945 -1.1905026 1.1120842 4.7433275 4.5386861 -2.7947142 0.33671682
+ 96000 28.021114 -1.0341645 0.6663033 4.2397505 4.6203984 -1.9904034 0.10972565
+ 97000 28.382022 -1.3916008 1.180588 4.0729621 4.6741792 -2.554927 0.13462346
+ 98000 27.895969 -0.7496449 1.3072185 4.2611888 4.3726077 -2.1320701 0.15376665
+ 99000 28.517889 -1.2183957 1.279778 3.957647 4.2638434 -2.2888407 0.042705003
+ 100000 28.109211 -1.2538948 0.83671785 4.3734766 4.544545 -2.3076497 0.042189096
+Loop time of 2.96683 on 1 procs for 100000 steps with 34 atoms
+
+Performance: 5824.390 ns/day, 0.004 hours/ns, 33705.963 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.98759 | 0.98759 | 0.98759 | 0.0 | 33.29
+Bond | 1.6463 | 1.6463 | 1.6463 | 0.0 | 55.49
+Neigh | 0.007688 | 0.007688 | 0.007688 | 0.0 | 0.26
+Comm | 0.012214 | 0.012214 | 0.012214 | 0.0 | 0.41
+Output | 0.0010295 | 0.0010295 | 0.0010295 | 0.0 | 0.03
+Modify | 0.25684 | 0.25684 | 0.25684 | 0.0 | 8.66
+Other | | 0.05519 | | | 1.86
+
+Nlocal: 34 ave 34 max 34 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 395 ave 395 max 395 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 395
+Ave neighs/atom = 11.6176
+Ave special neighs/atom = 9.52941
+Neighbor list builds = 237
+Dangerous builds = 0
+Total wall time: 0:00:02
diff --git a/examples/cmap/log.23Sep16.cmap.g++.4 b/examples/cmap/log.23Sep16.cmap.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..2d3efa66c6b156ada65d04c675a8ab80c2658066
--- /dev/null
+++ b/examples/cmap/log.23Sep16.cmap.g++.4
@@ -0,0 +1,200 @@
+LAMMPS (21 Sep 2016)
+# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016
+
+units real
+neigh_modify delay 2 every 1
+#newton off
+
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style charmm
+dihedral_style charmm
+improper_style harmonic
+
+pair_style lj/charmm/coul/charmm 8 12
+#pair_style lj/charmmfsw/coul/charmmfsh 8 12
+pair_modify mix arithmetic
+
+fix cmap all cmap charmm22.cmap
+fix_modify cmap energy yes
+
+read_data gagg.data fix cmap crossterm CMAP
+ orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 34 atoms
+ scanning bonds ...
+ 4 = max bonds/atom
+ scanning angles ...
+ 6 = max angles/atom
+ scanning dihedrals ...
+ 12 = max dihedrals/atom
+ scanning impropers ...
+ 1 = max impropers/atom
+ reading bonds ...
+ 33 bonds
+ reading angles ...
+ 57 angles
+ reading dihedrals ...
+ 75 dihedrals
+ reading impropers ...
+ 7 impropers
+ 4 = max # of 1-2 neighbors
+ 7 = max # of 1-3 neighbors
+ 13 = max # of 1-4 neighbors
+ 16 = max # of special neighbors
+
+special_bonds charmm
+fix 1 all nve
+
+#fix 1 all nvt temp 300 300 100.0
+#fix 2 all shake 1e-9 500 0 m 1.0
+
+velocity all create 0.0 12345678 dist uniform
+
+thermo 1000
+thermo_style custom step ecoul evdwl ebond eangle edihed f_cmap eimp
+timestep 2.0
+
+run 100000
+Neighbor list info ...
+ 1 neighbor list requests
+ update every 1 steps, delay 2 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 14
+ ghost atom cutoff = 14
+ binsize = 7 -> bins = 12 12 12
+Memory usage per processor = 15.9307 Mbytes
+Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro
+ 0 26.542777 -0.93822087 1.2470497 4.8441789 4.5432816 -1.473352 0.10453023
+ 1000 28.673005 -0.47724367 0.80029132 3.151679 4.4684446 -2.3928648 0.18604953
+ 2000 27.67955 -1.170342 0.72018905 4.0400131 4.4713764 -2.5490207 0.21834436
+ 3000 29.256656 -0.35856055 0.73303546 3.7411606 4.4710568 -2.8939692 0.37728884
+ 4000 30.097549 -1.1353905 0.79007053 3.0688444 4.4091469 -2.3383587 0.20743631
+ 5000 28.357525 -1.0723742 0.9180297 3.6579424 4.8792663 -2.3185572 0.088366962
+ 6000 29.214175 -0.95299239 0.81926011 3.6805428 4.6742897 -2.9343578 0.26697816
+ 7000 27.018614 -0.52423469 0.72502751 3.8840141 4.7780958 -2.3916014 0.24952572
+ 8000 29.682494 -1.0940368 0.76113051 3.1089345 4.9357863 -2.5662256 0.14112613
+ 9000 27.853918 -0.7913741 0.79503268 4.2177256 4.146792 -2.00475 0.090585666
+ 10000 27.13754 -0.80551128 1.1325023 4.4718283 5.2460631 -3.4947725 0.11893125
+ 11000 28.277434 -1.4897448 0.90075953 4.1895717 4.3594269 -1.9553119 0.090222212
+ 12000 28.630973 -1.222206 0.67796385 3.3905661 4.9691334 -2.9052721 0.13897658
+ 13000 28.593007 -0.95684026 0.75585196 3.7242568 4.7417932 -2.3893117 0.2074121
+ 14000 26.147115 -0.6026921 0.93591488 5.1292829 4.9821952 -2.2571835 0.11872421
+ 15000 26.29432 -0.82424162 1.048979 4.5569495 5.1189308 -2.9750422 0.16195676
+ 16000 29.189992 -0.80998247 0.74093508 3.8299275 4.4536688 -2.5497538 0.19155639
+ 17000 25.878012 -0.3519646 1.0988924 4.7359591 5.3923098 -2.7211029 0.13405223
+ 18000 27.726135 -0.28229987 0.63072344 4.1777888 4.7237271 -2.2177157 0.15939372
+ 19000 27.153504 -0.66477422 0.77910129 4.2036117 5.113851 -2.3494315 0.094793307
+ 20000 28.044833 -1.2835827 0.88745367 3.9955526 4.5077788 -3.0116467 0.17197859
+ 21000 27.205696 -0.74090037 1.0023251 4.3421733 4.912671 -2.3473271 0.26089356
+ 22000 27.385785 -0.93740972 0.84554838 4.562743 4.883866 -2.2110955 0.11573301
+ 23000 27.05534 -0.95605442 0.96719024 3.9277618 5.0359014 -2.6135949 0.21368061
+ 24000 28.273378 -0.97543103 0.8983443 4.2067985 4.4782971 -2.4230505 0.30311692
+ 25000 27.477789 -0.20383849 0.8380706 3.8037992 4.8312504 -2.5831791 0.093843746
+ 26000 30.344199 -1.9773473 0.92882437 3.7821405 4.5176677 -2.3020968 0.2194307
+ 27000 27.32767 -0.9803839 0.92988865 3.7611603 5.0328211 -2.4647656 0.18213622
+ 28000 27.34208 -1.037938 0.74488346 4.1727342 4.7056812 -2.2718346 0.17741362
+ 29000 27.682777 -0.51006495 0.57074224 4.7332237 4.7080462 -2.0491512 0.2130517
+ 30000 24.925731 0.13670248 0.84976065 4.4143762 6.0677158 -3.5479173 0.28059419
+ 31000 28.623419 -0.90725708 1.0710501 3.6930688 4.6639301 -2.2225373 0.20988139
+ 32000 27.732286 -1.1948367 0.89230134 4.4398373 4.8923907 -3.5849327 0.49167488
+ 33000 28.800772 -1.5319589 0.93455495 4.1634728 4.6107706 -2.3503486 0.22636535
+ 34000 27.374398 -1.0957453 0.89450276 3.9829508 4.991786 -2.3548834 0.15869465
+ 35000 28.38753 -0.89261166 0.90000776 3.536864 4.4293294 -2.4218118 0.10640557
+ 36000 27.713974 0.088038031 0.85190574 3.8969601 4.6256355 -2.7935475 0.34671662
+ 37000 29.13007 -1.378597 0.74412556 3.131538 4.6458653 -2.9373734 0.38035616
+ 38000 28.556573 -1.4055344 1.139984 4.0035753 4.2938358 -2.489329 0.25338326
+ 39000 26.447036 -1.1829705 0.87032438 5.0804461 4.5772023 -2.7346466 0.32165802
+ 40000 27.991454 -0.64295679 0.61020872 4.165871 4.4623087 -2.2244194 0.13826991
+ 41000 29.483296 -1.2400745 0.66926627 3.3473666 4.5766617 -2.3051145 0.12171554
+ 42000 26.948627 -1.2162288 1.1440628 4.3993073 5.1176533 -2.4734485 0.15497709
+ 43000 28.04459 -0.26543193 0.83647367 3.5160747 4.6964397 -2.2805068 0.12618821
+ 44000 28.213608 -1.216128 0.9132792 4.0206483 4.9483599 -2.3387049 0.10132022
+ 45000 28.283506 -1.0390766 0.86113772 4.504509 4.7209088 -2.3043085 0.14588362
+ 46000 27.433853 -0.57912107 0.78448334 4.5998579 5.1181394 -2.6165094 0.18722528
+ 47000 27.552939 -1.1128925 0.80087638 4.3448001 4.8062869 -2.4296883 0.2702479
+ 48000 28.874034 -1.3242519 0.71770727 3.5648565 4.4671824 -2.2608958 0.16115978
+ 49000 29.216186 -1.2210307 0.76937497 3.9260628 4.7550577 -2.7316081 0.085505664
+ 50000 28.065856 -1.1545547 0.86953819 4.4137666 4.732157 -2.4450867 0.23320539
+ 51000 26.308975 -0.99728352 0.90408444 4.2400186 5.6340425 -2.2090554 0.079882158
+ 52000 28.517571 -1.5027398 0.83520278 3.8176552 4.3001251 -2.0731682 0.1665375
+ 53000 28.77579 -1.3564268 0.97253881 3.6866407 4.8532347 -2.5330776 0.17668411
+ 54000 29.135315 -1.0994106 0.67605671 3.6819254 4.3134408 -1.9796929 0.076951331
+ 55000 26.168938 -0.76247492 0.88784685 4.6533473 6.0484793 -2.1334561 0.036876985
+ 56000 27.471775 -0.68648837 1.0576168 4.0354311 4.4767052 -2.2368959 0.24950568
+ 57000 29.787083 -1.4914384 1.0702944 3.5388133 4.5173097 -2.6694464 0.27937092
+ 58000 28.705448 -1.3016617 0.63337853 3.9552713 4.4119825 -1.8774657 0.17540021
+ 59000 29.130155 -0.91647363 0.84384883 3.1076903 4.5346348 -2.3457338 0.16674486
+ 60000 26.874199 -0.81598034 1.3432151 5.1322624 4.9545484 -2.9566615 0.25950486
+ 61000 27.401306 -0.82895856 1.1636949 4.020154 4.5745928 -2.601466 0.18061051
+ 62000 28.930313 -1.5231967 0.85173243 4.3517328 4.4878662 -2.5859205 0.1755493
+ 63000 26.56874 0.026147233 0.60836216 4.4231618 4.4390677 -2.1721849 0.08594237
+ 64000 26.729023 -0.76953985 0.76734633 4.5104288 5.0886456 -2.2118551 0.11339216
+ 65000 28.900471 -1.3901477 0.86194657 4.2774976 4.498325 -2.3672362 0.20668335
+ 66000 26.884253 -0.21198879 0.98509625 4.0843117 4.4344172 -2.3289416 0.23631017
+ 67000 27.210888 -0.84075559 1.0396559 4.7253607 4.4314589 -2.2985702 0.19326507
+ 68000 28.042102 -1.1898715 1.053534 3.8748712 4.4358449 -2.3998723 0.2431659
+ 69000 28.939141 -1.6968936 0.98155912 4.0460838 5.0075204 -2.5547087 0.28645131
+ 70000 27.15577 -0.85202797 1.1469079 4.7645212 4.6133209 -2.3410451 0.086576572
+ 71000 25.507417 -0.27780727 0.95157881 4.8759406 4.853401 -2.9598705 0.41011008
+ 72000 29.804703 -1.4847015 0.96345767 3.6797304 4.3678377 -2.4594626 0.14480206
+ 73000 28.602798 -1.4906143 0.72497266 4.2442974 4.5360598 -2.3621638 0.14385651
+ 74000 28.4928 -0.91319873 1.0377472 3.8033127 4.3991601 -2.4051911 0.095567428
+ 75000 26.38168 -0.70733237 1.1557817 5.697939 4.5935618 -2.4285007 0.058980519
+ 76000 27.16626 -0.83631031 0.84844246 4.7460887 4.5801472 -2.1260014 0.12845946
+ 77000 29.040661 -1.3089499 0.80285084 4.664804 4.5215895 -2.6861939 0.13215598
+ 78000 27.477871 -1.0600977 0.88595045 4.6264017 5.4095605 -2.474411 0.10987174
+ 79000 26.151797 -0.55779685 0.91382436 4.99964 4.9184022 -2.2547241 0.22854038
+ 80000 28.14523 -0.54460026 0.8982411 3.5374555 4.3785673 -2.3196807 0.088567964
+ 81000 29.029941 -1.6467789 0.79042284 3.7269899 4.7407998 -2.3795824 0.1408727
+ 82000 27.920287 -0.72798032 1.0076975 3.4449461 4.5621371 -2.8239074 0.25103454
+ 83000 29.131054 -1.114367 0.76887285 3.459639 4.5163922 -2.607825 0.19991648
+ 84000 28.249768 -0.69944068 1.0510846 4.0436296 4.6430538 -2.4213355 0.077299966
+ 85000 28.06888 -0.62132922 0.91829312 4.1294147 4.3099557 -2.354063 0.15866186
+ 86000 28.664264 -1.1022906 0.87831695 4.5773522 4.6045802 -2.9206875 0.33950063
+ 87000 27.960967 -1.2852756 0.77694253 3.9011301 4.9114139 -3.2374868 0.3068138
+ 88000 27.190678 -1.2803268 1.1545301 4.5769709 5.2404761 -2.3825838 0.10356039
+ 89000 26.792931 -0.44516641 1.0236244 4.2007253 4.7098685 -2.3608551 0.034447062
+ 90000 27.173991 -0.87185611 1.065719 4.1953618 4.6856408 -2.6539232 0.16957757
+ 91000 28.626528 -1.239257 0.89524651 4.7048012 4.6344201 -2.7367901 0.43534143
+ 92000 27.661812 -1.109044 0.92817391 5.0294489 4.3890711 -2.4108669 0.12570139
+ 93000 28.156793 -1.0820907 0.92812693 4.938385 4.4901426 -2.4023366 0.30135781
+ 94000 28.842149 -1.3524969 1.1451109 4.3125908 4.6959035 -2.6747199 0.2254607
+ 95000 27.862247 -1.2119045 1.0218976 4.2614082 4.4931316 -2.6902934 0.16345201
+ 96000 27.084973 -0.93738328 1.3984324 4.5647189 4.4232205 -2.2834097 0.11217888
+ 97000 27.587078 -0.89397255 0.78218462 3.8944421 4.3981479 -2.4205318 0.16570942
+ 98000 27.981746 -1.2380545 0.84847869 4.311441 4.7340377 -2.4270441 0.023565612
+ 99000 27.476625 -0.8569146 0.82550381 4.1656963 4.4064921 -2.4169708 0.160814
+ 100000 26.121325 -0.63610855 1.0803389 4.9257118 4.7073263 -2.4010334 0.066303044
+Loop time of 2.60487 on 4 procs for 100000 steps with 34 atoms
+
+Performance: 6633.735 ns/day, 0.004 hours/ns, 38389.667 timesteps/s
+99.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.066848 | 0.26055 | 0.6843 | 48.6 | 10.00
+Bond | 0.067332 | 0.45486 | 0.93545 | 55.1 | 17.46
+Neigh | 0.0078266 | 0.007863 | 0.0078835 | 0.0 | 0.30
+Comm | 0.41829 | 1.3207 | 1.8951 | 50.8 | 50.70
+Output | 0.0033038 | 0.0036355 | 0.0040481 | 0.4 | 0.14
+Modify | 0.040861 | 0.15162 | 0.27091 | 27.3 | 5.82
+Other | | 0.4057 | | | 15.57
+
+Nlocal: 8.5 ave 15 max 2 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Nghost: 25.5 ave 32 max 19 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Neighs: 98.75 ave 257 max 18 min
+Histogram: 1 1 1 0 0 0 0 0 0 1
+
+Total # of neighbors = 395
+Ave neighs/atom = 11.6176
+Ave special neighs/atom = 9.52941
+Neighbor list builds = 294
+Dangerous builds = 0
+Total wall time: 0:00:02
diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..39081168d8103eecb22d42868cf6afe37286dfba
--- /dev/null
+++ b/src/MOLECULE/fix_cmap.cpp
@@ -0,0 +1,1432 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Implementation of the CHARMM CMAP; adds an extra energy term for the
+ peptide backbone dihedrals. The tools/ch2lmp.pl conversion script, which
+ generates an extra section in the LAMMPS data file, is needed in order to
+ generate the info used by this fix style.
+
+ Contributing authors:
+ Xiaohu Hu, CMB/ORNL (hux2@ornl.gov)
+ David Hyde-Volpe, Tigran Abramyan, and Robert A. Latour (Clemson University)
+ Chris Lorenz (Kings College-London)
+
+ References:
+ - MacKerell et al., J. Am. Chem. Soc. 126(2004):698-699.
+ - MacKerell et al., J. Comput. Chem. 25(2004):1400-1415.
+ -------------------------------------------------------------------------*/
+
+#include "mpi.h"
+#include "math.h"
+#include "stdlib.h"
+#include "string.h"
+#include "stdio.h"
+#include "fix_cmap.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "update.h"
+#include "respa.h"
+#include "modify.h"
+#include "domain.h"
+#include "force.h"
+#include "group.h"
+#include "comm.h"
+#include "math_const.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+using namespace MathConst;
+
+#define MAXLINE 256
+#define LISTDELTA 10000
+#define LB_FACTOR 1.5
+
+#define CMAPMAX 6 // max # of CMAP terms stored by one atom
+#define CMAPDIM 24 // grid map dimension is 24 x 24
+#define CMAPXMIN -360.0
+#define CMAPXMIN2 -180.0
+#define CMAPDX 15.0 // 360/CMAPDIM
+
+/* ---------------------------------------------------------------------- */
+
+FixCMAP::FixCMAP(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
+{
+ if (narg != 4) error->all(FLERR,"Illegal fix cmap command");
+
+ restart_global = 1;
+ restart_peratom = 1;
+ peatom_flag = 1;
+ virial_flag = 1;
+ peratom_freq = 1;
+ scalar_flag = 1;
+ global_freq = 1;
+ extscalar = 1;
+ extvector = 1;
+ wd_header = 1;
+ wd_section = 1;
+
+ MPI_Comm_rank(world,&me);
+ MPI_Comm_size(world,&nprocs);
+
+ // allocate memory for CMAP data
+
+ memory->create(g_axis,CMAPDIM,"cmap:g_axis");
+ memory->create(cmapgrid,6,CMAPDIM,CMAPDIM,"cmap:grid");
+ memory->create(d1cmapgrid,6,CMAPDIM,CMAPDIM,"cmap:d1grid");
+ memory->create(d2cmapgrid,6,CMAPDIM,CMAPDIM,"cmap:d2grid");
+ memory->create(d12cmapgrid,6,CMAPDIM,CMAPDIM,"cmap:d12grid");
+
+ // read, initialize, broadcast cmapgrid
+
+ if (me == 0) read_grid_map(arg[3]);
+ MPI_Bcast(&cmapgrid[0][0][0],6*CMAPDIM*CMAPDIM,MPI_DOUBLE,0,world);
+
+ // perform initial allocation of atom-based arrays
+ // register with Atom class
+
+ num_crossterm = NULL;
+ crossterm_type = NULL;
+ crossterm_atom1 = NULL;
+ crossterm_atom2 = NULL;
+ crossterm_atom3 = NULL;
+ crossterm_atom4 = NULL;
+ crossterm_atom5 = NULL;
+
+ nmax_previous = 0;
+ grow_arrays(atom->nmax);
+ atom->add_callback(0);
+ atom->add_callback(1);
+
+ // local list of crossterms
+
+ ncmap = 0;
+ maxcrossterm = 0;
+ crosstermlist = NULL;
+}
+
+/* --------------------------------------------------------------------- */
+
+FixCMAP::~FixCMAP()
+{
+ // unregister callbacks to this fix from Atom class
+
+ atom->delete_callback(id,0);
+ atom->delete_callback(id,1);
+
+ memory->destroy(g_axis);
+ memory->destroy(cmapgrid);
+ memory->destroy(d1cmapgrid);
+ memory->destroy(d2cmapgrid);
+ memory->destroy(d12cmapgrid);
+
+ memory->destroy(crosstermlist);
+
+ memory->destroy(num_crossterm);
+ memory->destroy(crossterm_type);
+ memory->destroy(crossterm_atom1);
+ memory->destroy(crossterm_atom2);
+ memory->destroy(crossterm_atom3);
+ memory->destroy(crossterm_atom4);
+ memory->destroy(crossterm_atom5);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixCMAP::setmask()
+{
+ int mask = 0;
+ mask |= PRE_NEIGHBOR;
+ mask |= PRE_REVERSE;
+ mask |= POST_FORCE;
+ mask |= THERMO_ENERGY;
+ mask |= POST_FORCE_RESPA;
+ mask |= MIN_POST_FORCE;
+ return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixCMAP::init()
+{
+ int i;
+ double angle;
+
+ i = 0;
+ angle = -180.0;
+ while (angle < 180.0) {
+ g_axis[i] = angle;
+ angle += CMAPDX;
+ i++;
+ }
+
+ // pre-compute the derivatives of the maps
+
+ for (i = 0; i < 6; i++)
+ set_map_derivatives(cmapgrid[i],d1cmapgrid[i],d2cmapgrid[i],d12cmapgrid[i]);
+
+ // define newton_bond here in case restart file was read (not data file)
+
+ newton_bond = force->newton_bond;
+}
+
+/* --------------------------------------------------------------------- */
+
+void FixCMAP::setup(int vflag)
+{
+ pre_neighbor();
+
+ if (strstr(update->integrate_style,"verlet"))
+ post_force(vflag);
+ else {
+ ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
+ post_force_respa(vflag,nlevels_respa-1,0);
+ ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
+ }
+}
+
+/* --------------------------------------------------------------------- */
+
+void FixCMAP::setup_pre_neighbor()
+{
+ pre_neighbor();
+}
+
+/* --------------------------------------------------------------------- */
+
+void FixCMAP::min_setup(int vflag)
+{
+ pre_neighbor();
+ post_force(vflag);
+}
+
+/* ----------------------------------------------------------------------
+ store local neighbor list as if newton_bond = OFF, even if actually ON
+------------------------------------------------------------------------- */
+
+void FixCMAP::pre_neighbor()
+{
+ int i,m,itype,atom1,atom2,atom3,atom4,atom5;
+
+ // guesstimate initial length of local crossterm list
+ // if ncmap was not set (due to read_restart, no read_data),
+ // then list will grow by LISTDELTA chunks
+
+ if (maxcrossterm == 0) {
+ if (nprocs == 1) maxcrossterm = ncmap;
+ else maxcrossterm = static_cast<int> (LB_FACTOR*ncmap/nprocs);
+ memory->create(crosstermlist,maxcrossterm,6,"cmap:crosstermlist");
+ }
+
+ int nlocal = atom->nlocal;
+
+ ncrosstermlist = 0;
+
+ for (i = 0; i < nlocal; i++) {
+ for (m = 0; m < num_crossterm[i]; m++) {
+ atom1 = atom->map(crossterm_atom1[i][m]);
+ atom2 = atom->map(crossterm_atom2[i][m]);
+ atom3 = atom->map(crossterm_atom3[i][m]);
+ atom4 = atom->map(crossterm_atom4[i][m]);
+ atom5 = atom->map(crossterm_atom5[i][m]);
+
+ if (atom1 == -1 || atom2 == -1 || atom3 == -1 ||
+ atom4 == -1 || atom5 == -1) {
+ char str[128];
+ sprintf(str,"CMAP atoms "
+ TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
+ crossterm_atom1[i][m],crossterm_atom2[i][m],
+ crossterm_atom3[i][m],crossterm_atom4[i][m],
+ crossterm_atom5[i][m],me,update->ntimestep);
+ error->one(FLERR,str);
+ }
+ atom1 = domain->closest_image(i,atom1);
+ atom2 = domain->closest_image(i,atom2);
+ atom3 = domain->closest_image(i,atom3);
+ atom4 = domain->closest_image(i,atom4);
+ atom5 = domain->closest_image(i,atom5);
+
+ if (i <= atom1 && i <= atom2 && i <= atom3 &&
+ i <= atom4 && i <= atom5) {
+ if (ncrosstermlist == maxcrossterm) {
+ maxcrossterm += LISTDELTA;
+ memory->grow(crosstermlist,maxcrossterm,6,"cmap:crosstermlist");
+ }
+ crosstermlist[ncrosstermlist][0] = atom1;
+ crosstermlist[ncrosstermlist][1] = atom2;
+ crosstermlist[ncrosstermlist][2] = atom3;
+ crosstermlist[ncrosstermlist][3] = atom4;
+ crosstermlist[ncrosstermlist][4] = atom5;
+ crosstermlist[ncrosstermlist][5] = crossterm_type[i][m];
+ ncrosstermlist++;
+ }
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ store eflag, so can use it in post_force to tally per-atom energies
+------------------------------------------------------------------------- */
+
+void FixCMAP::pre_reverse(int eflag, int vflag)
+{
+ eflag_caller = eflag;
+}
+
+/* ----------------------------------------------------------------------
+ compute CMAP terms as if newton_bond = OFF, even if actually ON
+------------------------------------------------------------------------- */
+
+void FixCMAP::post_force(int vflag)
+{
+ int n,i1,i2,i3,i4,i5,type,nlist;
+ int li1, li2, mli1,mli2,mli11,mli21,t1,li3,li4,mli3,mli4,mli31,mli41;
+ int list[5];
+ // vectors needed to calculate the cross-term dihedral angles
+ double vb21x,vb21y,vb21z,vb32x,vb32y,vb32z,vb34x,vb34y,vb34z;
+ double vb23x,vb23y,vb23z;
+ double vb43x,vb43y,vb43z,vb45x,vb45y,vb45z,a1x,a1y,a1z,b1x,b1y,b1z;
+ double a2x,a2y,a2z,b2x,b2y,b2z,r32,a1sq,b1sq,a2sq,b2sq,dpr21r32,dpr34r32;
+ double dpr32r43,dpr45r43,r43,vb12x,vb12y,vb12z,vb54x,vb54y,vb54z;
+ // cross-term dihedral angles
+ double phi,psi,phi1,psi1;
+ double f1[3],f2[3],f3[3],f4[3],f5[3],vcmap[6];
+ double gs[4],d1gs[4],d2gs[4],d12gs[4];
+ double engfraction;
+ // vectors needed for the gradient/force calculation
+ double dphidr1x,dphidr1y,dphidr1z,dphidr2x,dphidr2y,dphidr2z;
+ double dphidr3x,dphidr3y,dphidr3z,dphidr4x,dphidr4y,dphidr4z;
+ double dpsidr1x,dpsidr1y,dpsidr1z,dpsidr2x,dpsidr2y,dpsidr2z;
+ double dpsidr3x,dpsidr3y,dpsidr3z,dpsidr4x,dpsidr4y,dpsidr4z;
+
+ // Definition of cross-term dihedrals
+
+ // phi dihedral
+ // |--------------------|
+ // a1-----a2-----a3-----a4-----a5 cross-term atoms
+ // C N CA C N cross-term atom types
+ // |--------------------|
+ // psi dihedral
+
+ double **x = atom->x;
+ double **f = atom->f;
+ int nlocal = atom->nlocal;
+
+ ecmap = 0.0;
+ int eflag = eflag_caller;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = 0;
+
+ for (n = 0; n < ncrosstermlist; n++) {
+ i1 = crosstermlist[n][0];
+ i2 = crosstermlist[n][1];
+ i3 = crosstermlist[n][2];
+ i4 = crosstermlist[n][3];
+ i5 = crosstermlist[n][4];
+
+ type = crosstermlist[n][5];
+ if (type == 0) continue;
+
+ // calculate bond vectors for both dihedrals
+
+ // phi
+ // vb21 = r2 - r1
+
+ vb21x = x[i2][0] - x[i1][0];
+ vb21y = x[i2][1] - x[i1][1];
+ vb21z = x[i2][2] - x[i1][2];
+ vb12x = -1.0*vb21x;
+ vb12y = -1.0*vb21y;
+ vb12z = -1.0*vb21z;
+ vb32x = x[i3][0] - x[i2][0];
+ vb32y = x[i3][1] - x[i2][1];
+ vb32z = x[i3][2] - x[i2][2];
+ vb23x = -1.0*vb32x;
+ vb23y = -1.0*vb32y;
+ vb23z = -1.0*vb32z;
+
+ vb34x = x[i3][0] - x[i4][0];
+ vb34y = x[i3][1] - x[i4][1];
+ vb34z = x[i3][2] - x[i4][2];
+
+ // psi
+ // bond vectors same as for phi: vb32
+
+ vb43x = -1.0*vb34x;
+ vb43y = -1.0*vb34y;
+ vb43z = -1.0*vb34z;
+
+ vb45x = x[i4][0] - x[i5][0];
+ vb45y = x[i4][1] - x[i5][1];
+ vb45z = x[i4][2] - x[i5][2];
+ vb54x = -1.0*vb45x;
+ vb54y = -1.0*vb45y;
+ vb54z = -1.0*vb45z;
+
+ // calculate normal vectors for planes that define the dihedral angles
+
+ a1x = vb12y*vb23z - vb12z*vb23y;
+ a1y = vb12z*vb23x - vb12x*vb23z;
+ a1z = vb12x*vb23y - vb12y*vb23x;
+
+ b1x = vb43y*vb23z - vb43z*vb23y;
+ b1y = vb43z*vb23x - vb43x*vb23z;
+ b1z = vb43x*vb23y - vb43y*vb23x;
+
+ a2x = vb23y*vb34z - vb23z*vb34y;
+ a2y = vb23z*vb34x - vb23x*vb34z;
+ a2z = vb23x*vb34y - vb23y*vb34x;
+
+ b2x = vb45y*vb43z - vb45z*vb43y;
+ b2y = vb45z*vb43x - vb45x*vb43z;
+ b2z = vb45x*vb43y - vb45y*vb43x;
+
+ // calculate terms used later in calculations
+
+ r32 = sqrt(vb32x*vb32x + vb32y*vb32y + vb32z*vb32z);
+ a1sq = a1x*a1x + a1y*a1y + a1z*a1z;
+ b1sq = b1x*b1x + b1y*b1y + b1z*b1z;
+
+ r43 = sqrt(vb43x*vb43x + vb43y*vb43y + vb43z*vb43z);
+ a2sq = a2x*a2x + a2y*a2y + a2z*a2z;
+ b2sq = b2x*b2x + b2y*b2y + b2z*b2z;
+ //if (a1sq<0.0001 || b1sq<0.0001 || a2sq<0.0001 || b2sq<0.0001)
+ // printf("a1sq b1sq a2sq b2sq: %f %f %f %f \n",a1sq,b1sq,a2sq,b2sq);
+ if (a1sq<0.0001 || b1sq<0.0001 || a2sq<0.0001 || b2sq<0.0001) continue;
+ dpr21r32 = vb21x*vb32x + vb21y*vb32y + vb21z*vb32z;
+ dpr34r32 = vb34x*vb32x + vb34y*vb32y + vb34z*vb32z;
+ dpr32r43 = vb32x*vb43x + vb32y*vb43y + vb32z*vb43z;
+ dpr45r43 = vb45x*vb43x + vb45y*vb43y + vb45z*vb43z;
+
+ // calculate the backbone dihedral angles as VMD and GROMACS
+
+ phi = dihedral_angle_atan2(vb21x,vb21y,vb21z,a1x,a1y,a1z,b1x,b1y,b1z,r32);
+ psi = dihedral_angle_atan2(vb32x,vb32y,vb32z,a2x,a2y,a2z,b2x,b2y,b2z,r43);
+
+ if (phi == 180.0) phi= -180.0;
+ if (psi == 180.0) psi= -180.0;
+
+ phi1 = phi;
+ if (phi1 < 0.0) phi1 += 360.0;
+ psi1 = psi;
+ if (psi1 < 0.0) psi1 += 360.0;
+
+ // find the neighbor grid point index
+
+ li1 = int(((phi1+CMAPXMIN2)/CMAPDX)+((CMAPDIM*1.0)/2.0));
+ li2 = int(((psi1+CMAPXMIN2)/CMAPDX)+((CMAPDIM*1.0)/2.0));
+
+ li3 = int((phi-CMAPXMIN2)/CMAPDX);
+ li4 = int((psi-CMAPXMIN2)/CMAPDX);
+ mli3 = li3 % CMAPDIM;
+ mli4 = li4 % CMAPDIM;
+ mli31 = (li3+1) % CMAPDIM;
+ mli41 = (li4+1) %CMAPDIM;
+ mli1 = li1 % CMAPDIM;
+ mli2 = li2 % CMAPDIM;
+ mli11 = (li1+1) % CMAPDIM;
+ mli21 = (li2+1) %CMAPDIM;
+ t1 = type-1;
+ if (t1 < 0 || t1 > 5) error->all(FLERR,"Invalid CMAP crossterm_type");
+
+ // determine the values and derivatives for the grid square points
+
+ gs[0] = cmapgrid[t1][mli3][mli4];
+ gs[1] = cmapgrid[t1][mli31][mli4];
+ gs[2] = cmapgrid[t1][mli31][mli41];
+ gs[3] = cmapgrid[t1][mli3][mli41];
+ d1gs[0] = d1cmapgrid[t1][mli1][mli2];
+ d1gs[1] = d1cmapgrid[t1][mli11][mli2];
+ d1gs[2] = d1cmapgrid[t1][mli11][mli21];
+ d1gs[3] = d1cmapgrid[t1][mli1][mli21];
+
+ d2gs[0] = d2cmapgrid[t1][mli1][mli2];
+ d2gs[1] = d2cmapgrid[t1][mli11][mli2];
+ d2gs[2] = d2cmapgrid[t1][mli11][mli21];
+ d2gs[3] = d2cmapgrid[t1][mli1][mli21];
+
+ d12gs[0] = d12cmapgrid[t1][mli1][mli2];
+ d12gs[1] = d12cmapgrid[t1][mli11][mli2];
+ d12gs[2] = d12cmapgrid[t1][mli11][mli21];
+ d12gs[3] = d12cmapgrid[t1][mli1][mli21];
+
+ // calculate the cmap energy and the gradient (dE/dphi,dE/dpsi)
+
+ bc_interpol(phi,psi,li3,li4,gs,d1gs,d2gs,d12gs);
+
+ // sum up cmap energy contributions
+
+ engfraction = 0.2 * E;
+ if (i1 < nlocal) ecmap += engfraction;
+ if (i2 < nlocal) ecmap += engfraction;
+ if (i3 < nlocal) ecmap += engfraction;
+ if (i4 < nlocal) ecmap += engfraction;
+ if (i5 < nlocal) ecmap += engfraction;
+
+ // calculate the derivatives dphi/dr_i
+
+ dphidr1x = 1.0*r32/a1sq*a1x;
+ dphidr1y = 1.0*r32/a1sq*a1y;
+ dphidr1z = 1.0*r32/a1sq*a1z;
+
+ dphidr2x = -1.0*r32/a1sq*a1x - dpr21r32/a1sq/r32*a1x +
+ dpr34r32/b1sq/r32*b1x;
+ dphidr2y = -1.0*r32/a1sq*a1y - dpr21r32/a1sq/r32*a1y +
+ dpr34r32/b1sq/r32*b1y;
+ dphidr2z = -1.0*r32/a1sq*a1z - dpr21r32/a1sq/r32*a1z +
+ dpr34r32/b1sq/r32*b1z;
+
+ dphidr3x = dpr34r32/b1sq/r32*b1x - dpr21r32/a1sq/r32*a1x - r32/b1sq*b1x;
+ dphidr3y = dpr34r32/b1sq/r32*b1y - dpr21r32/a1sq/r32*a1y - r32/b1sq*b1y;
+ dphidr3z = dpr34r32/b1sq/r32*b1z - dpr21r32/a1sq/r32*a1z - r32/b1sq*b1z;
+
+ dphidr4x = r32/b1sq*b1x;
+ dphidr4y = r32/b1sq*b1y;
+ dphidr4z = r32/b1sq*b1z;
+
+ // calculate the derivatives dpsi/dr_i
+
+ dpsidr1x = 1.0*r43/a2sq*a2x;
+ dpsidr1y = 1.0*r43/a2sq*a2y;
+ dpsidr1z = 1.0*r43/a2sq*a2z;
+
+ dpsidr2x = r43/a2sq*a2x + dpr32r43/a2sq/r43*a2x - dpr45r43/b2sq/r43*b2x;
+ dpsidr2y = r43/a2sq*a2y + dpr32r43/a2sq/r43*a2y - dpr45r43/b2sq/r43*b2y;
+ dpsidr2z = r43/a2sq*a2z + dpr32r43/a2sq/r43*a2z - dpr45r43/b2sq/r43*b2z;
+
+ dpsidr3x = dpr45r43/b2sq/r43*b2x - dpr32r43/a2sq/r43*a2x - r43/b2sq*b2x;
+ dpsidr3y = dpr45r43/b2sq/r43*b2y - dpr32r43/a2sq/r43*a2y - r43/b2sq*b2y;
+ dpsidr3z = dpr45r43/b2sq/r43*b2z - dpr32r43/a2sq/r43*a2z - r43/b2sq*b2z;
+
+ dpsidr4x = r43/b2sq*b2x;
+ dpsidr4y = r43/b2sq*b2y;
+ dpsidr4z = r43/b2sq*b2z;
+
+ // calculate forces on cross-term atoms: F = -(dE/dPhi)*(dPhi/dr)
+
+ f1[0] = dEdPhi*dphidr1x;
+ f1[1] = dEdPhi*dphidr1y;
+ f1[2] = dEdPhi*dphidr1z;
+ f2[0] = dEdPhi*dphidr2x + dEdPsi*dpsidr1x;
+ f2[1] = dEdPhi*dphidr2y + dEdPsi*dpsidr1y;
+ f2[2] = dEdPhi*dphidr2z + dEdPsi*dpsidr1z;
+ f3[0] = -dEdPhi*dphidr3x - dEdPsi*dpsidr2x;
+ f3[1] = -dEdPhi*dphidr3y - dEdPsi*dpsidr2y;
+ f3[2] = -dEdPhi*dphidr3z - dEdPsi*dpsidr2z;
+ f4[0] = -dEdPhi*dphidr4x - dEdPsi*dpsidr3x;
+ f4[1] = -dEdPhi*dphidr4y - dEdPsi*dpsidr3y;
+ f4[2] = -dEdPhi*dphidr4z - dEdPsi*dpsidr3z;
+ f5[0] = -dEdPsi*dpsidr4x;
+ f5[1] = -dEdPsi*dpsidr4y;
+ f5[2] = -dEdPsi*dpsidr4z;
+
+ // apply force to each of the 5 atoms
+
+ if (i1 < nlocal) {
+ f[i1][0] += f1[0];
+ f[i1][1] += f1[1];
+ f[i1][2] += f1[2];
+ }
+ if (i2 < nlocal) {
+ f[i2][0] += f2[0];
+ f[i2][1] += f2[1];
+ f[i2][2] += f2[2];
+ }
+ if (i3 < nlocal) {
+ f[i3][0] += f3[0];
+ f[i3][1] += f3[1];
+ f[i3][2] += f3[2];
+ }
+ if (i4 < nlocal) {
+ f[i4][0] += f4[0];
+ f[i4][1] += f4[1];
+ f[i4][2] += f4[2];
+ }
+ if (i5 < nlocal) {
+ f[i5][0] += f5[0];
+ f[i5][1] += f5[1];
+ f[i5][2] += f5[2];
+ }
+
+ // tally energy and/or virial
+
+ if (evflag) {
+ nlist = 0;
+ if (i1 < nlocal) list[nlist++] = i1;
+ if (i2 < nlocal) list[nlist++] = i2;
+ if (i3 < nlocal) list[nlist++] = i3;
+ if (i4 < nlocal) list[nlist++] = i4;
+ if (i5 < nlocal) list[nlist++] = i5;
+ vcmap[0] = (vb12x*f1[0])+(vb32x*f3[0])+((vb43x+vb32x)*f4[0])+
+ ((vb54x+vb43x+vb32x)*f5[0]);
+ vcmap[1] = (vb12y*f1[1])+(vb32y*f3[1])+((vb43y+vb32y)*f4[1])+
+ ((vb54y+vb43y+vb32y)*f5[1]);
+ vcmap[2] = (vb12z*f1[2])+(vb32z*f3[2])+((vb43z+vb32z)*f4[2])+
+ ((vb54z+vb43z+vb32z)*f5[2]);
+ vcmap[3] = (vb12x*f1[1])+(vb32x*f3[1])+((vb43x+vb32x)*f4[1])+
+ ((vb54x+vb43x+vb32x)*f5[1]);
+ vcmap[4] = (vb12x*f1[2])+(vb32x*f3[2])+((vb43x+vb32x)*f4[2])+
+ ((vb54x+vb43x+vb32x)*f5[2]);
+ vcmap[5] = (vb12y*f1[2])+(vb32y*f3[2])+((vb43y+vb32y)*f4[2])+
+ ((vb54y+vb43y+vb32y)*f5[2]);
+ ev_tally(nlist,list,5.0,E,vcmap);
+ //ev_tally(5,list,nlocal,newton_bond,E,vcmap);
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixCMAP::post_force_respa(int vflag, int ilevel, int iloop)
+{
+ if (ilevel == nlevels_respa-1) post_force(vflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixCMAP::min_post_force(int vflag)
+{
+ post_force(vflag);
+}
+
+/* ----------------------------------------------------------------------
+ energy of CMAP term
+------------------------------------------------------------------------- */
+
+double FixCMAP::compute_scalar()
+{
+ double all;
+ MPI_Allreduce(&ecmap,&all,1,MPI_DOUBLE,MPI_SUM,world);
+ return all;
+}
+
+// ----------------------------------------------------------------------
+// ----------------------------------------------------------------------
+// methods to read CMAP potential file, perform interpolation
+// ----------------------------------------------------------------------
+// ----------------------------------------------------------------------
+
+void FixCMAP::read_grid_map(char *cmapfile)
+{
+ char line[MAXLINE];
+ char *chunk;
+ int i1, i2, i3, i4, i5, i6, j1, j2, j3, j4, j5, j6, counter;
+
+ FILE *fp = fopen(cmapfile,"r");
+ if (fp == NULL) {
+ char str[128];
+ sprintf(str,"Cannot open fix cmap file %s",cmapfile);
+ error->one(FLERR,str);
+ }
+
+ for (int ix1 = 0; ix1 < 6; ix1++)
+ for (int ix2 = 0; ix2 < CMAPDIM; ix2++)
+ for (int ix3 = 0; ix3 < CMAPDIM; ix3++)
+ cmapgrid[ix1][ix2][ix3] = 0.0;
+
+ counter = 0;
+ i1 = i2 = i3 = i4 = i5 = i6 = 0;
+ j1 = j2 = j3 = j4 = j5 = j6 = 0;
+
+ while (fgets(line,MAXLINE,fp) != NULL) {
+ if (line == "" || line[0] == '#') { ;; }
+
+ // read in the cmap grid point values
+ // NOTE: The order to read the 6 grid maps is HARD-CODED, thus errors
+ // will occur if content of the file "cmap.data" is altered
+ //
+ // Reading order of the maps:
+ // 1. Alanine map
+ // 2. Alanine before proline map
+ // 3. Proline map
+ // 4. Two adjacent prolines map
+ // 5. Glycine map
+ // 6. Glycine before proline map
+
+ else {
+ chunk = strtok(line, " \r\n");
+ while (chunk != NULL) {
+
+ // alanine map
+
+ if (counter < CMAPDIM*CMAPDIM) {
+ cmapgrid[0][i1][j1] = atof(chunk);
+ chunk = strtok(NULL, " \r\n");
+ j1++;
+ if (j1 == CMAPDIM) {
+ j1 = 0;
+ i1++;
+ }
+ counter++;
+ }
+
+ // alanine-proline map
+
+ else if (counter >= CMAPDIM*CMAPDIM &&
+ counter < 2*CMAPDIM*CMAPDIM) {
+ cmapgrid[1][i2][j2]= atof(chunk);
+ chunk = strtok(NULL, " \r\n");
+ j2++;
+ if (j2 == CMAPDIM) {
+ j2 = 0;
+ i2++;
+ }
+ counter++;
+ }
+
+ // proline map
+
+ else if (counter >= 2*CMAPDIM*CMAPDIM &&
+ counter < 3*CMAPDIM*CMAPDIM) {
+ cmapgrid[2][i3][j3] = atof(chunk);
+ chunk = strtok(NULL, " \r\n");
+ j3++;
+ if (j3 == CMAPDIM) {
+ j3 = 0;
+ i3++;
+ }
+ counter++;
+ }
+
+ // 2 adjacent prolines map
+
+ else if (counter >= 3*CMAPDIM*CMAPDIM &&
+ counter < 4*CMAPDIM*CMAPDIM) {
+ cmapgrid[3][i4][j4] = atof(chunk);
+ chunk = strtok(NULL, " \r\n");
+ j4++;
+ if (j4 == CMAPDIM) {
+ j4 = 0;
+ i4++;
+ }
+ counter++;
+ }
+
+ // glycine map
+
+ else if (counter >= 4*CMAPDIM*CMAPDIM &&
+ counter < 5*CMAPDIM*CMAPDIM) {
+ cmapgrid[4][i5][j5] = atof(chunk);
+ chunk = strtok(NULL, " \r\n");
+ j5++;
+ if (j5 == CMAPDIM) {
+ j5 = 0;
+ i5++;
+ }
+ counter++;
+ }
+
+ // glycine-proline map
+
+ else if (counter >= 5*CMAPDIM*CMAPDIM &&
+ counter < 6*CMAPDIM*CMAPDIM) {
+ cmapgrid[5][i6][j6] = atof(chunk);
+ chunk = strtok(NULL, " \r\n");
+ j6++;
+ if (j6 == CMAPDIM) {
+ j6 = 0;
+ i6++;
+ }
+ counter++;
+ }
+
+ else break;
+ }
+ }
+ }
+
+ fclose(fp);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixCMAP::spline(double *y, double *ddy, int n)
+{
+ // create the 2nd dervatives of a taublated function y_i(x_i)
+ // at the tabulated points
+
+ int i, j;
+ double p, *u;
+
+ memory->create(u,n-1,"cmap:u");
+
+ ddy[0] = u[0] = 0.0;
+
+ for (i = 1; i <= n-2; i++) {
+ p = 1.0/(ddy[i-1]+4.0);
+ ddy[i] = -p;
+ u[i] = ((((6.0*y[i+1])-(12.0*y[i])+(6.0*y[i-1]))/(CMAPDX*CMAPDX))-u[i-1])*p;
+ }
+
+ ddy[n-1] = 0.0;
+
+ for (j = n-2; j >= 0; j--)
+ ddy[j] = ddy[j]*ddy[j+1] + u[j];
+
+ memory->destroy(u);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixCMAP::spl_interpolate(double x, double *y, double *ddy, double &yo,
+ double &dyo)
+{
+ // perform a 1D cubic spline interpolation
+
+ int ix;
+ double a,b,a1,b1,a2,b2;
+
+ ix = int((x-CMAPXMIN)/CMAPDX-(1./2.));
+
+ a = (CMAPXMIN+(ix*1.0)*CMAPDX-x)/CMAPDX;
+ b = (x-CMAPXMIN-(((ix-1)*1.0)*CMAPDX))/CMAPDX;
+
+ a1 = a*a*a-a;
+ b1 = b*b*b-b;
+
+ a2 = 3.0*a*a-1.0;
+ b2 = 3.0*b*b-1.0;
+ yo = a*y[ix]+b*y[ix+1]+(a1*ddy[ix]+b1*ddy[ix+1])*(CMAPDX*CMAPDX)/6.0;
+ dyo = (y[ix+1]-y[ix])/CMAPDX-a2/6.0*CMAPDX*ddy[ix]+b2/6.0*CMAPDX*ddy[ix+1];
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixCMAP::set_map_derivatives(double **map, double **d1yo, double **d2yo,
+ double **d12yo)
+{
+ // precompute the gradient and cross-derivatives of the map grid points.
+ // use the bicubic spline to calculate the derivatives
+
+ int i, j, k, ii, jj, xm, p;
+ double phi, psi, y, d1y, d2y, d12y, tyyk,tdyk;
+ double *tmp_y, *tmp_dy, *tmp_ddy, **tmap, **tddmap;
+ int ix;
+ double a,b,a1,b1,a2,b2;
+
+ xm = CMAPDIM/2;
+ p = CMAPDIM;
+
+ y = 0.;
+ d1y = 0.;
+ d2y = 0.;
+ d12y = 0.;
+
+ memory->create(tmp_y,CMAPDIM*2,"cmap:tmp_y");
+ memory->create(tmp_dy,CMAPDIM*2,"cmap:tmp_dy");
+ memory->create(tmp_ddy,CMAPDIM*2,"cmap:tmp_ddy");
+ memory->create(tmap,CMAPDIM*2,CMAPDIM*2,"cmap:tmap");
+ memory->create(tddmap,CMAPDIM*2,CMAPDIM*2,"cmap:tddmap");
+
+ // periodically expand the original map
+ // use the expanded map for bicubic spline interpolation,
+ // which is used to obtain the derivatives
+ // actual interpolation is done with bicubic interpolation
+
+ for (i = 0; i < CMAPDIM*2; i++) {
+ ii = ((i+CMAPDIM-xm)%CMAPDIM);
+ for (j = 0; j < CMAPDIM*2; j++) {
+ jj = ((j+CMAPDIM-xm)%CMAPDIM);
+ tmap[i][j] = map[ii][jj];
+ }
+ }
+
+ for (i = 0; i < CMAPDIM*2; i++)
+ spline(tmap[i], tddmap[i], CMAPDIM*2);
+
+ for (i = xm; i < CMAPDIM+xm; i++) {
+ phi = (i-xm)*CMAPDX-180.0;
+ for (j = xm; j < CMAPDIM+xm; j++) {
+ psi = (j-xm)*CMAPDX-180.0;
+ ix = int((psi-CMAPXMIN)/CMAPDX);
+ a = (CMAPXMIN+((ix+1)*1.0)*CMAPDX-psi)/CMAPDX;
+ b = (psi-CMAPXMIN-((ix)*1.0)*CMAPDX)/CMAPDX;
+ a1 = a*a*a-a;
+ b1 = b*b*b-b;
+ a2 = 3.0*a*a-1.0;
+ b2 = 3.0*b*b-1.0;
+ for (k = 0; k < CMAPDIM*2; k++) {
+ tyyk = tmp_y[k];
+ tdyk = tmp_dy[k];
+ tyyk = a*tmap[k][ix]+b*tmap[k][ix+1]+
+ (a1*tddmap[k][ix]+b1*tddmap[k][ix+1])*(CMAPDX*CMAPDX)/6.0;
+ tdyk = (tmap[k][ix+1]-tmap[k][ix])/CMAPDX-
+ (a2/6.0*CMAPDX*tddmap[k][ix])+(b2/6.0*CMAPDX*tddmap[k][ix+1]);
+ tmp_y[k] = tyyk;
+ tmp_dy[k] = tdyk;
+ }
+
+ spline(tmp_y,tmp_ddy,CMAPDIM+xm+xm);
+ ix = int((phi-CMAPXMIN)/CMAPDX);
+ a = (CMAPXMIN+((ix+1)*1.0)*CMAPDX-phi)/CMAPDX;
+ b = (phi-CMAPXMIN-(ix*1.0)*CMAPDX)/CMAPDX;
+ a1 = a*a*a-a;
+ b1 = b*b*b-b;
+ a2 = 3.0*a*a-1.0;
+ b2 = 3.0*b*b-1.0;
+ y = a*tmp_y[ix]+b*tmp_y[ix+1]+
+ (a1*tmp_ddy[ix]+b1*tmp_ddy[ix+1])*(CMAPDX*CMAPDX)/6.0;
+ d1y = (tmp_y[ix+1]-tmp_y[ix])/CMAPDX-
+ a2/6.0*CMAPDX*tmp_ddy[ix]+b2/6.0*CMAPDX*tmp_ddy[ix+1];
+ spline(tmp_dy,tmp_ddy,CMAPDIM+xm+xm);
+ ix = int((phi-CMAPXMIN)/CMAPDX);
+ a = (CMAPXMIN+((ix+1)*1.0)*CMAPDX-phi)/CMAPDX;
+ b = (phi-CMAPXMIN-(ix*1.0)*CMAPDX)/CMAPDX;
+ a1 = a*a*a-a;
+ b1 = b*b*b-b;
+ a2 = 3.0*a*a-1.0;
+ b2 = 3.0*b*b-1.0;
+ d2y = a*tmp_dy[ix]+b*tmp_dy[ix+1]+
+ (a1*tmp_ddy[ix]+b1*tmp_ddy[ix+1])*(CMAPDX*CMAPDX)/6.0;
+ d12y = (tmp_dy[ix+1]-tmp_dy[ix])/CMAPDX-
+ a2/6.0*CMAPDX*tmp_ddy[ix]+b2/6.0*CMAPDX*tmp_ddy[ix+1];
+ d1yo[i%p][j%p] = d1y;
+ d2yo[i%p][j%p] = d2y;
+ d12yo[i%p][j%p] = d12y;
+ }
+ }
+
+ memory->destroy(tmp_y);
+ memory->destroy(tmp_dy);
+ memory->destroy(tmp_ddy);
+ memory->destroy(tmap);
+ memory->destroy(tddmap);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double FixCMAP::dihedral_angle_atan2(double fx, double fy, double fz,
+ double ax, double ay, double az,
+ double bx, double by, double bz,
+ double absg)
+{
+ // calculate the dihedral angle
+
+ double angle, arg1, arg2;
+
+ arg1 = absg*(fx*bx+fy*by+fz*bz);
+ arg2 = ax*bx+ay*by+az*bz;
+
+ if (arg1 == 0 && arg2 == 0)
+ error->all(FLERR,"CMAP: atan2 function cannot take 2 zero arguments");
+ else {
+ angle = atan2(arg1,arg2);
+ angle = angle*180.0/MY_PI;
+ }
+
+ return angle;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixCMAP::bc_coeff(double *gs, double *d1gs, double *d2gs, double *d12gs)
+{
+ // calculate the bicubic interpolation coefficients c_ij
+
+ static int wt[16][16] =
+ { 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
+ -3, 0, 0, 3, 0, 0, 0, 0,-2, 0, 0,-1, 0, 0, 0, 0,
+ 2, 0, 0,-2, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0,
+ 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
+ 0, 0, 0, 0,-3, 0, 0, 3, 0, 0, 0, 0,-2, 0, 0,-1,
+ 0, 0, 0, 0, 2, 0, 0,-2, 0, 0, 0, 0, 1, 0, 0, 1,
+ -3, 3, 0, 0,-2,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0,-3, 3, 0, 0,-2,-1, 0, 0,
+ 9,-9, 9,-9, 6, 3,-3,-6, 6,-6,-3, 3, 4, 2, 1, 2,
+ -6, 6,-6, 6,-4,-2, 2, 4,-3, 3, 3,-3,-2,-1,-1,-2,
+ 2,-2, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 2,-2, 0, 0, 1, 1, 0, 0,
+ -6, 6,-6, 6,-3,-3, 3, 3,-4, 4, 2,-2,-2,-2,-1,-1,
+ 4,-4, 4,-4, 2, 2,-2,-2, 2,-2,-2, 2, 1, 1, 1, 1
+ };
+
+ int i, j, k, l, in;
+ double xx, x[16];
+
+ for (i = 0; i < 4; i++) {
+ x[i] = gs[i];
+ x[i+4] = d1gs[i]*CMAPDX;
+ x[i+8] = d2gs[i]*CMAPDX;
+ x[i+12] = d12gs[i]*CMAPDX*CMAPDX;
+ }
+
+ in = 0;
+ for (i = 0; i < 4; i++) {
+ for (j = 0; j < 4; j++) {
+ xx = 0.0;
+ for (k = 0; k < 16; k++) xx += wt[in][k]*x[k];
+ in++;
+ cij[i][j] = xx;
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixCMAP::bc_interpol(double x1, double x2, int low1, int low2, double *gs,
+ double *d1gs, double *d2gs, double *d12gs)
+{
+ // for a given point of interest and its corresponding grid square values,
+ // gradients and cross-derivatives
+ // calculate the interpolated value of the point of interest (POI)
+
+ int i, p=12;
+ double t, u, fac, gs1l, gs2l, gs1u, gs2u;
+
+ // set the interpolation coefficients
+
+ bc_coeff(gs,d1gs,d2gs,d12gs);
+
+ gs1l = g_axis[low1];
+ gs2l = g_axis[low2];
+
+ t = (x1-gs1l)/CMAPDX;
+ u = (x2-gs2l)/CMAPDX;
+
+ E = dEdPhi = dEdPsi = 0.0;
+
+ for (i = 3; i >= 0; i--) {
+ E = t*E + ((cij[i][3]*u+cij[i][2])*u+cij[i][1])*u+cij[i][0];
+ dEdPhi = u*dEdPhi + (3.0*cij[3][i]*t+2.0*cij[2][i])*t+cij[1][i];
+ dEdPsi = t*dEdPsi + (3.0*cij[i][3]*u+2.0*cij[i][2])*u+cij[i][1];
+ }
+
+ dEdPhi *= (180.0/MY_PI/CMAPDX);
+ dEdPsi *= (180.0/MY_PI/CMAPDX);
+}
+
+// ----------------------------------------------------------------------
+// ----------------------------------------------------------------------
+// methods to read and write data file
+// ----------------------------------------------------------------------
+// ----------------------------------------------------------------------
+
+void FixCMAP::read_data_header(char *line)
+{
+ if (strstr(line,"crossterms")) {
+ sscanf(line,BIGINT_FORMAT,&ncmap);
+ } else error->all(FLERR,"Invalid read data header line for fix cmap");
+
+ // didn't set in constructor b/c this fix could be defined
+ // before newton command
+
+ newton_bond = force->newton_bond;
+}
+
+/* ----------------------------------------------------------------------
+ unpack N lines in buf from section of data file labeled by keyword
+ id_offset is applied to atomID fields if multiple data files are read
+ store CMAP interactions as if newton_bond = OFF, even if actually ON
+------------------------------------------------------------------------- */
+
+void FixCMAP::read_data_section(char *keyword, int n, char *buf,
+ tagint id_offset)
+{
+ int m,tmp,itype;
+ tagint atom1,atom2,atom3,atom4,atom5;
+ char *next;
+
+ next = strchr(buf,'\n');
+ *next = '\0';
+ int nwords = atom->count_words(buf);
+ *next = '\n';
+
+ if (nwords != 7) {
+ char str[128];
+ sprintf(str,"Incorrect %s format in data file",keyword);
+ error->all(FLERR,str);
+ }
+
+ // loop over lines of CMAP crossterms
+ // tokenize the line into values
+ // add crossterm to one of my atoms, depending on newton_bond
+
+ for (int i = 0; i < n; i++) {
+ next = strchr(buf,'\n');
+ *next = '\0';
+ sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
+ " " TAGINT_FORMAT " " TAGINT_FORMAT,
+ &tmp,&itype,&atom1,&atom2,&atom3,&atom4,&atom5);
+
+ atom1 += id_offset;
+ atom2 += id_offset;
+ atom3 += id_offset;
+ atom4 += id_offset;
+ atom5 += id_offset;
+
+ if ((m = atom->map(atom1)) >= 0) {
+ if (num_crossterm[m] == CMAPMAX)
+ error->one(FLERR,"Too many CMAP crossterms for one atom");
+ crossterm_type[m][num_crossterm[m]] = itype;
+ crossterm_atom1[m][num_crossterm[m]] = atom1;
+ crossterm_atom2[m][num_crossterm[m]] = atom2;
+ crossterm_atom3[m][num_crossterm[m]] = atom3;
+ crossterm_atom4[m][num_crossterm[m]] = atom4;
+ crossterm_atom5[m][num_crossterm[m]] = atom5;
+ num_crossterm[m]++;
+ }
+
+ if ((m = atom->map(atom2)) >= 0) {
+ if (num_crossterm[m] == CMAPMAX)
+ error->one(FLERR,"Too many CMAP crossterms for one atom");
+ crossterm_type[m][num_crossterm[m]] = itype;
+ crossterm_atom1[m][num_crossterm[m]] = atom1;
+ crossterm_atom2[m][num_crossterm[m]] = atom2;
+ crossterm_atom3[m][num_crossterm[m]] = atom3;
+ crossterm_atom4[m][num_crossterm[m]] = atom4;
+ crossterm_atom5[m][num_crossterm[m]] = atom5;
+ num_crossterm[m]++;
+ }
+
+ if ((m = atom->map(atom3)) >= 0) {
+ if (num_crossterm[m] == CMAPMAX)
+ error->one(FLERR,"Too many CMAP crossterms for one atom");
+ crossterm_type[m][num_crossterm[m]] = itype;
+ crossterm_atom1[m][num_crossterm[m]] = atom1;
+ crossterm_atom2[m][num_crossterm[m]] = atom2;
+ crossterm_atom3[m][num_crossterm[m]] = atom3;
+ crossterm_atom4[m][num_crossterm[m]] = atom4;
+ crossterm_atom5[m][num_crossterm[m]] = atom5;
+ num_crossterm[m]++;
+ }
+
+ if ((m = atom->map(atom4)) >= 0) {
+ if (num_crossterm[m] == CMAPMAX)
+ error->one(FLERR,"Too many CMAP crossterms for one atom");
+ crossterm_type[m][num_crossterm[m]] = itype;
+ crossterm_atom1[m][num_crossterm[m]] = atom1;
+ crossterm_atom2[m][num_crossterm[m]] = atom2;
+ crossterm_atom3[m][num_crossterm[m]] = atom3;
+ crossterm_atom4[m][num_crossterm[m]] = atom4;
+ crossterm_atom5[m][num_crossterm[m]] = atom5;
+ num_crossterm[m]++;
+ }
+
+ if ((m = atom->map(atom5)) >= 0) {
+ if (num_crossterm[m] == CMAPMAX)
+ error->one(FLERR,"Too many CMAP crossterms for one atom");
+ crossterm_type[m][num_crossterm[m]] = itype;
+ crossterm_atom1[m][num_crossterm[m]] = atom1;
+ crossterm_atom2[m][num_crossterm[m]] = atom2;
+ crossterm_atom3[m][num_crossterm[m]] = atom3;
+ crossterm_atom4[m][num_crossterm[m]] = atom4;
+ crossterm_atom5[m][num_crossterm[m]] = atom5;
+ num_crossterm[m]++;
+ }
+
+ buf = next + 1;
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+bigint FixCMAP::read_data_skip_lines(char *keyword)
+{
+ return ncmap;
+}
+
+/* ----------------------------------------------------------------------
+ write Mth header line to file
+ only called by proc 0
+------------------------------------------------------------------------- */
+
+void FixCMAP::write_data_header(FILE *fp, int mth)
+{
+ fprintf(fp,BIGINT_FORMAT " cmap crossterms\n",ncmap);
+}
+
+/* ----------------------------------------------------------------------
+ return size I own for Mth data section
+ # of data sections = 1 for this fix
+ nx = # of crossterms owned by my local atoms
+ if newton_bond off, atom only owns crossterm if it is atom3
+ ny = columns = type + 5 atom IDs
+------------------------------------------------------------------------- */
+
+void FixCMAP::write_data_section_size(int mth, int &nx, int &ny)
+{
+ int i,m;
+
+ tagint *tag = atom->tag;
+ int nlocal = atom->nlocal;
+
+ nx = 0;
+ for (i = 0; i < nlocal; i++)
+ for (m = 0; m < num_crossterm[i]; m++)
+ if (crossterm_atom3[i][m] == tag[i]) nx++;
+
+ ny = 6;
+}
+
+/* ----------------------------------------------------------------------
+ pack values for Mth data section into 2d buf
+ buf allocated by caller as owned crossterms by 6
+------------------------------------------------------------------------- */
+
+void FixCMAP::write_data_section_pack(int mth, double **buf)
+{
+ int i,m;
+
+ // 1st column = CMAP type
+ // 2nd-6th columns = 5 atom IDs
+
+ tagint *tag = atom->tag;
+ int nlocal = atom->nlocal;
+
+ int n = 0;
+ for (i = 0; i < nlocal; i++) {
+ for (m = 0; m < num_crossterm[i]; m++) {
+ if (crossterm_atom3[i][m] != tag[i]) continue;
+ buf[n][0] = ubuf(crossterm_type[i][m]).d;
+ buf[n][1] = ubuf(crossterm_atom1[i][m]).d;
+ buf[n][2] = ubuf(crossterm_atom2[i][m]).d;
+ buf[n][3] = ubuf(crossterm_atom3[i][m]).d;
+ buf[n][4] = ubuf(crossterm_atom4[i][m]).d;
+ buf[n][5] = ubuf(crossterm_atom5[i][m]).d;
+ n++;
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ write section keyword for Mth data section to file
+ use Molecules or Charges if that is only field, else use fix ID
+ only called by proc 0
+------------------------------------------------------------------------- */
+
+void FixCMAP::write_data_section_keyword(int mth, FILE *fp)
+{
+ fprintf(fp,"\nCMAP\n\n");
+}
+
+/* ----------------------------------------------------------------------
+ write N lines from buf to file
+ convert buf fields to int or double depending on styles
+ index can be used to prepend global numbering
+ only called by proc 0
+------------------------------------------------------------------------- */
+
+void FixCMAP::write_data_section(int mth, FILE *fp,
+ int n, double **buf, int index)
+{
+ for (int i = 0; i < n; i++)
+ fprintf(fp,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT
+ " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT "\n",
+ index+i,(int) ubuf(buf[i][0]).i,(tagint) ubuf(buf[i][1]).i,
+ (tagint) ubuf(buf[i][2]).i,(tagint) ubuf(buf[i][3]).i,
+ (tagint) ubuf(buf[i][4]).i,(tagint) ubuf(buf[i][5]).i);
+}
+
+// ----------------------------------------------------------------------
+// ----------------------------------------------------------------------
+// methods for restart and communication
+// ----------------------------------------------------------------------
+// ----------------------------------------------------------------------
+
+/* ----------------------------------------------------------------------
+ pack entire state of Fix into one write
+------------------------------------------------------------------------- */
+
+void FixCMAP::write_restart(FILE *fp)
+{
+ if (comm->me == 0) {
+ int size = sizeof(bigint);
+ fwrite(&size,sizeof(int),1,fp);
+ fwrite(&ncmap,sizeof(bigint),1,fp);
+ }
+}
+
+/* ----------------------------------------------------------------------
+ use state info from restart file to restart the Fix
+------------------------------------------------------------------------- */
+
+void FixCMAP::restart(char *buf)
+{
+ ncmap = *((bigint *) buf);
+}
+
+/* ----------------------------------------------------------------------
+ pack values in local atom-based arrays for restart file
+------------------------------------------------------------------------- */
+
+int FixCMAP::pack_restart(int i, double *buf)
+{
+ int n = 1;
+ for (int m = 0; m < num_crossterm[i]; m++) {
+ buf[n++] = ubuf(MAX(crossterm_type[i][m],-crossterm_type[i][m])).d;
+ buf[n++] = ubuf(crossterm_atom1[i][m]).d;
+ buf[n++] = ubuf(crossterm_atom2[i][m]).d;
+ buf[n++] = ubuf(crossterm_atom3[i][m]).d;
+ buf[n++] = ubuf(crossterm_atom4[i][m]).d;
+ buf[n++] = ubuf(crossterm_atom5[i][m]).d;
+ }
+ buf[0] = n;
+
+ return n;
+}
+
+/* ----------------------------------------------------------------------
+ unpack values from atom->extra array to restart the fix
+------------------------------------------------------------------------- */
+
+void FixCMAP::unpack_restart(int nlocal, int nth)
+{
+ double **extra = atom->extra;
+
+ // skip to Nth set of extra values
+
+ int n = 0;
+ for (int i = 0; i < nth; i++) n += static_cast<int> (extra[nlocal][n]);
+
+ int count = static_cast<int> (extra[nlocal][n++]);
+ num_crossterm[nlocal] = (count-1)/6;
+
+ for (int m = 0; m < num_crossterm[nlocal]; m++) {
+ crossterm_type[nlocal][m] = (int) ubuf(extra[nlocal][n++]).i;
+ crossterm_atom1[nlocal][m] = (tagint) ubuf(extra[nlocal][n++]).i;
+ crossterm_atom2[nlocal][m] = (tagint) ubuf(extra[nlocal][n++]).i;
+ crossterm_atom3[nlocal][m] = (tagint) ubuf(extra[nlocal][n++]).i;
+ crossterm_atom4[nlocal][m] = (tagint) ubuf(extra[nlocal][n++]).i;
+ crossterm_atom5[nlocal][m] = (tagint) ubuf(extra[nlocal][n++]).i;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ maxsize of any atom's restart data
+------------------------------------------------------------------------- */
+
+int FixCMAP::maxsize_restart()
+{
+ return 1 + CMAPMAX*6;
+}
+
+/* ----------------------------------------------------------------------
+ size of atom nlocal's restart data
+------------------------------------------------------------------------- */
+
+int FixCMAP::size_restart(int nlocal)
+{
+ return 1 + num_crossterm[nlocal]*6;
+}
+
+/* ----------------------------------------------------------------------
+ allocate atom-based array
+------------------------------------------------------------------------- */
+
+void FixCMAP::grow_arrays(int nmax)
+{
+ num_crossterm = memory->grow(num_crossterm,nmax,"cmap:num_crossterm");
+ crossterm_type = memory->grow(crossterm_type,nmax,CMAPMAX,
+ "cmap:crossterm_type");
+ crossterm_atom1 = memory->grow(crossterm_atom1,nmax,CMAPMAX,
+ "cmap:crossterm_atom1");
+ crossterm_atom2 = memory->grow(crossterm_atom2,nmax,CMAPMAX,
+ "cmap:crossterm_atom2");
+ crossterm_atom3 = memory->grow(crossterm_atom3,nmax,CMAPMAX,
+ "cmap:crossterm_atom3");
+ crossterm_atom4 = memory->grow(crossterm_atom4,nmax,CMAPMAX,
+ "cmap:crossterm_atom4");
+ crossterm_atom5 = memory->grow(crossterm_atom5,nmax,CMAPMAX,
+ "cmap:crossterm_atom5");
+
+ // must initialize num_crossterm to 0 for added atoms
+ // may never be set for some atoms when data file is read
+
+ for (int i = nmax_previous; i < nmax; i++) num_crossterm[i] = 0;
+ nmax_previous = nmax;
+}
+
+/* ----------------------------------------------------------------------
+ copy values within local atom-based array
+------------------------------------------------------------------------- */
+
+void FixCMAP::copy_arrays(int i, int j, int delflag)
+{
+ num_crossterm[j] = num_crossterm[i];
+
+ for (int k = 0; k < num_crossterm[j]; k++){
+ crossterm_type[j][k] = crossterm_type[i][k];
+ crossterm_atom1[j][k] = crossterm_atom1[i][k];
+ crossterm_atom2[j][k] = crossterm_atom2[i][k];
+ crossterm_atom3[j][k] = crossterm_atom3[i][k];
+ crossterm_atom4[j][k] = crossterm_atom4[i][k];
+ crossterm_atom5[j][k] = crossterm_atom5[i][k];
+ }
+}
+
+/* ----------------------------------------------------------------------
+ initialize one atom's array values, called when atom is created
+------------------------------------------------------------------------- */
+
+void FixCMAP::set_arrays(int i)
+{
+ num_crossterm[i] = 0;
+}
+
+/* ----------------------------------------------------------------------
+ pack values in local atom-based array for exchange with another proc
+------------------------------------------------------------------------- */
+
+int FixCMAP::pack_exchange(int i, double *buf)
+{
+ int n = 0;
+ buf[n++] = ubuf(num_crossterm[i]).d;
+ for (int m = 0; m < num_crossterm[i]; m++) {
+ buf[n++] = ubuf(crossterm_type[i][m]).d;
+ buf[n++] = ubuf(crossterm_atom1[i][m]).d;
+ buf[n++] = ubuf(crossterm_atom2[i][m]).d;
+ buf[n++] = ubuf(crossterm_atom3[i][m]).d;
+ buf[n++] = ubuf(crossterm_atom4[i][m]).d;
+ buf[n++] = ubuf(crossterm_atom5[i][m]).d;
+ }
+ return n;
+}
+
+/* ----------------------------------------------------------------------
+ unpack values in local atom-based array from exchange with another proc
+------------------------------------------------------------------------- */
+
+int FixCMAP::unpack_exchange(int nlocal, double *buf)
+{
+ int n = 0;
+ num_crossterm[nlocal] = (int) ubuf(buf[n++]).i;
+ for (int m = 0; m < num_crossterm[nlocal]; m++) {
+ crossterm_type[nlocal][m] = (int) ubuf(buf[n++]).i;
+ crossterm_atom1[nlocal][m] = (tagint) ubuf(buf[n++]).i;
+ crossterm_atom2[nlocal][m] = (tagint) ubuf(buf[n++]).i;
+ crossterm_atom3[nlocal][m] = (tagint) ubuf(buf[n++]).i;
+ crossterm_atom4[nlocal][m] = (tagint) ubuf(buf[n++]).i;
+ crossterm_atom5[nlocal][m] = (tagint) ubuf(buf[n++]).i;
+ }
+ return n;
+}
+
+/* ----------------------------------------------------------------------
+ memory usage of local atom-based arrays
+------------------------------------------------------------------------- */
+
+double FixCMAP::memory_usage()
+{
+ int nmax = atom->nmax;
+ double bytes = nmax * sizeof(int); // num_crossterm
+ bytes += nmax*CMAPMAX * sizeof(int); // crossterm_type
+ bytes += 5*nmax*CMAPMAX * sizeof(int); // crossterm_atom 12345
+ bytes += maxcrossterm*6 * sizeof(int); // crosstermlist
+ return bytes;
+}
diff --git a/src/MOLECULE/fix_cmap.h b/src/MOLECULE/fix_cmap.h
new file mode 100644
index 0000000000000000000000000000000000000000..213d881e23c599e29165a8193f4f8d4efb31d87a
--- /dev/null
+++ b/src/MOLECULE/fix_cmap.h
@@ -0,0 +1,129 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(cmap,FixCMAP)
+
+#else
+
+#ifndef LMP_FIX_CMAP_H
+#define LMP_FIX_CMAP_H
+
+#include "fix.h"
+namespace LAMMPS_NS {
+
+class FixCMAP : public Fix {
+ public:
+ FixCMAP(class LAMMPS *, int, char **);
+ ~FixCMAP();
+ int setmask();
+ void init();
+ void setup(int);
+ void setup_pre_neighbor();
+ void min_setup(int);
+ void pre_neighbor();
+ void pre_reverse(int, int);
+ void post_force(int);
+ void post_force_respa(int, int, int);
+ void min_post_force(int);
+ double compute_scalar();
+
+ void read_data_header(char *);
+ void read_data_section(char *, int, char *, tagint);
+ bigint read_data_skip_lines(char *);
+ void write_data_header(FILE *, int);
+ void write_data_section_size(int, int &, int &);
+ void write_data_section_pack(int, double **);
+ void write_data_section_keyword(int, FILE *);
+ void write_data_section(int, FILE *, int, double **, int);
+
+ void write_restart(FILE *);
+ void restart(char *);
+ int pack_restart(int, double *);
+ void unpack_restart(int, int);
+ int size_restart(int);
+ int maxsize_restart();
+
+ void grow_arrays(int);
+ void copy_arrays(int, int, int);
+ void set_arrays(int);
+ int pack_exchange(int, double *);
+ int unpack_exchange(int, double *);
+
+ double memory_usage();
+
+ private:
+ int nprocs,me;
+ int newton_bond,eflag_caller;
+ int ctype,nlevels_respa;
+ int ncrosstermtypes,crossterm_per_atom,maxcrossterm;
+ int ncrosstermlist;
+ bigint ncmap;
+
+ int **crosstermlist;
+
+ int nmax_previous;
+ int *num_crossterm;
+ int **crossterm_type;
+ tagint **crossterm_atom1,**crossterm_atom2,**crossterm_atom3;
+ tagint **crossterm_atom4,**crossterm_atom5;
+
+ double E,dEdPhi,dEdPsi;
+ double ecmap;
+ double fcmap[4],cij[4][4];
+ double *g_axis;
+
+ // CMAP grid points obtained from external file
+
+ double ***cmapgrid;
+
+ // partial derivatives and cross-derivatives of the grid data
+
+ double ***d1cmapgrid,***d2cmapgrid,***d12cmapgrid;
+
+ // read map grid data
+
+ void read_grid_map(char *);
+
+ // read in CMAP cross terms from LAMMPS data file
+
+ void read_cmap_data(int, char *);
+
+ // pre-compute the partial and cross-derivatives of map grid points
+
+ void set_map_derivatives(double **, double **, double **, double **);
+
+ // cubic spline interpolation functions for derivatives of map grid points
+
+ void spline(double *, double *, int);
+ void spl_interpolate(double, double *, double *, double &, double &);
+
+ // calculate dihedral angles
+
+ double dihedral_angle_atan2(double, double, double, double, double, double,
+ double, double, double, double);
+
+ // calculate bicubic interpolation coefficient matrix c_ij
+
+ void bc_coeff(double *, double *, double *, double *);
+
+ // perform bicubic interpolation at point of interest
+
+ void bc_interpol(double, double, int, int, double *, double *, double *,
+ double *);
+};
+}
+
+#endif
+#endif
diff --git a/src/version.h b/src/version.h
index 3f90b4fc5bf56d29015582430bea194cbd8d6442..35c0f59e694ea868300abf5570bf3aef3e99ec10 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "21 Sep 2016"
+#define LAMMPS_VERSION "26 Sep 2016"
diff --git a/tools/ch2lmp/README b/tools/ch2lmp/README
index eb994ccb6fda4277c11b2ddef8609df05d08bc12..fa031bd7579a0e5a26ecf961735c2060fc252128 100755
--- a/tools/ch2lmp/README
+++ b/tools/ch2lmp/README
@@ -11,35 +11,40 @@ In this directory, you should find:
3) An "example" folder containing an example of how to use these tools.
4) An "other" folder containing other potentially useful tools.
-In addition, you will need to provide the following input for
+In addition, you will need to provide the following input for
charmm2lammps.pl:
+
1) a CHARMM parameter file (par_<forcefield>.prm)
2) a CHARMM topology file (top_<forcefield>.rtf)
3) a CHARMM coordinates file or pdb file (<project>.crd or <project>.pdb)
+ (NOTE: a .pdb file is required if the -cmap option is used)
4) a CHARMM psf file (<project>.psf)
To use the charmm2lammps.pl script, type: "perl charmm2lammps.pl
-[-option[=#]] <forcefield> <project>" where <forcefield> is the name
-of the CHARMM FF you are using, (i.e. all22_prot), and <project> is
-the common name of your *.crd and *.psf files. The options for the
-script are listed below. If the option requires a parameter, the
-syntax must be [-option[=#]], (i.e. -border=5).
-
--help "display available options",
--charmm "add charmm types to LAMMPS data file",
--water "add TIP3P water [default: 1 g/cc]",
--ions "add (counter)ions using Na+ and Cl- [default: 0 mol/l]",
--center "recenter atoms",
--quiet "do not print info",
--pdb_ctrl "output project_ctrl.pdb",
--l "set x-, y-, and z-dimensions simultaneously",
--lx "x-dimension of simulation box",
--ly "y-dimension of simulation box",
--lz "z-dimension of simulation box",
--border "add border to all sides of simulation box [default: 0 A]",
--ax "rotation around x-axis",
--ay "rotation around y-axis",
--az "rotation around z-axis"
+<forcefield> <project> [-option=value ...]" where <forcefield> is the
+name of the CHARMM FF you are using, (i.e. all22_prot), and <project>
+is the common name of your *.crd and *.psf files. Possible options
+are listed next. If the option requires a parameter, the syntax
+should be -option=value (e.g. -border=5).
+
+-help display available options
+-charmm add charmm types to LAMMPS data file
+-water add TIP3P water [default: 1 g/cc]
+-ions add (counter)ions using Na+ and Cl- [default: 0 mol/l]
+-center recenter atoms
+-quiet do not print info
+-pdb_ctrl output project_ctrl.pdb
+-l set x-, y-, and z-dimensions simultaneously
+-lx x-dimension of simulation box
+-ly y-dimension of simulation box
+-lz z-dimension of simulation box
+-border add border to all sides of simulation box [default: 0 A]
+-ax rotation around x-axis
+-ay rotation around y-axis
+-az rotation around z-axis
+-cd correction for dihedral for carbohydrate systems
+-cmap add CMAP section to data file and fix cmap command lines in
+ input script" (NOTE: requires use of *.pdb file)
In the "example" folder, you will find example files that were created
by following the steps below. These steps describe how to take a
@@ -100,7 +105,22 @@ molecule. The -pdb_ctrl option produces the 1ac7_ctrl.pdb file that
can be visualized in a standard visualization package such as VMD. The
-charmm option put comments into the LAMMPS data file (everything
after the # sign is a comment) for user convenience in tracking atom
-types etc. according to CHARMM nomenclature.
+types etc. according to CHARMM nomenclature.
+
+The example molecule provided above (i.e., 1ac7) is a DNA fragment.
+If instead, a peptide longer than 2 amino acid residues or a protein
+is to be modeled, the '-cmap' option should be used. This will add a
+section at the end of the data file with the heading of 'CMAP' that
+will contain cmap crossterm corrections for the phi-psi dihedrals for
+the amino acid residues. You will then need to also copy the
+appropriate file for the cmap crossterms into your directory and be
+sure that you are using the appropriate cmap crossterms that go with
+the respective version of the charmm force field that is being used
+(e.g, cmap22.data or cmap36.data). This is necessary to account for
+the fact that the CHARMM group has provided updated cmap correction
+terms for use with the c36 and more recent version of the charmm
+protein force field. Copies of cmap22.data and cmap36.data are
+provided in the tools/ch2lmp directory.
The default timestep in the LAMMPS *.in file is set to 0.5 fs, which
can typically be increased to 2 fs after equilibration if the bonds
@@ -109,9 +129,9 @@ delay on neigh_modify can probably increased to 5 or so to improve
speed.
The -ions option allows the user to neutralize the simulation cell
-with Na+ or Cl- counterions if the molecule has a net
-charge. Additional salt can be added by increasing the default
-concentration (i.e. -ions=0.5).
+with Na+ or Cl- counterions if the molecule has a net charge
+Additional salt can be added by increasing the default concentration
+(e.g. -ions=0.5).
** In the "other" file folder, you will find:
@@ -126,5 +146,3 @@ concentration (i.e. -ions=0.5).
3) A 3rd party perl script called "crd2pdb.pl"
4) A 3rd party fortran code called "pdb_to_crd.f"
-
-
diff --git a/tools/ch2lmp/charmm2lammps.pl b/tools/ch2lmp/charmm2lammps.pl
index 8e43a06cabd2d4807344cabe8395bc4988f84a51..0e39f589da06f0c098f45e34389804e3eecca241 100644
--- a/tools/ch2lmp/charmm2lammps.pl
+++ b/tools/ch2lmp/charmm2lammps.pl
@@ -28,22 +28,43 @@
# 20050630 Fixed symbol issues arising from salt addition
# 20060818 Changed reading of pdb format to read exact columns
# 20070109 Changed AddMass() to use $max_id correctly
-# 20160114 Added compatibility for parameter files that use IMPROPERS instead of IMPROPER
-# Print warning when not all parameters are detected. Set correct number of atom types.
-# 20160613 Fix off-by-one issue in atom type validation check
-# Replace -charmm command line flag with -nohints flag
-# and enable type hints in data file by default.
-# Add hints also to section headers
-# Add a brief minimization to example input template.
+# 20130508 Added 'CMAP crossterms' section at the end of the data file
+# 20131001 Added instructions in CMAP section to fix problem if 'ter'
+# is not designated in .pdb file to identify last amino acid
#
# General Many thanks to Paul S. Crozier for checking script validity
# against his projects.
+#
+# ------------------------------------------------------------------------------
+# NOTE: This current version was modified by Xiaohu Hu (hux2@ornl.gov)
+# DATE: April, May 2009
+# Then finalized to complete addition of CMAP terms to data file
+# by Robert A. Latour, Clemson University (latourr@clemson.edu)
+# and Chris Lorenz, King's College (chris.lorenz@kcl.ac.uk)
+# DATE: May, 2013
+#
+# The original code of charmm2lammps.pl is modified
+#
+# 1. to fix the double-counting problem in 1-4 interaction associated
+# with the carbon-hydrate 6-rings containing systems. (See subroutine
+# DihedralCorrect6Ring, activated with the option "-cd")
+#
+# 2. to add a new section "CMAP" which is a list of the peptide
+# backbone dihedrals cross terms. A modifed LAMMPS version will be
+# needed to be able to use this feature. (See subroutine CharmmCmap,
+# activated with the option "-cmap")
+#
+# These subroutines are independent from the original charmm2lammps.pl, i.e.
+# the original code of charmm2lammps.pl is unchanged. The new routines only
+# evaluate and modify the output generated by the original charmm2lammps.pl.
+# -----------------------------------------------------------------------------
+
# Initialization
sub Test
{
- my $name = shift(@_);
+ my $name = shift(@_); # "@_" = argument passed to the subroutine
printf("Error: file %s not found\n", $name) if (!scalar(stat($name)));
return !scalar(stat($name));
@@ -54,11 +75,13 @@
{
my $k = 0;
my @dir = ("x", "y", "z");
- my @options = ("-help", "-nohints", "-water", "-ions", "-center",
+
+ # Modified by Xiaohu Hu, May 2009. Options "-cmap" and "-cdihedral" added
+ my @options = ("-help", "-charmm", "-water", "-ions", "-center",
"-quiet", "-pdb_ctrl", "-l", "-lx", "-ly", "-lz",
- "-border", "-ax", "-ay", "-az");
- my @remarks = ("display this message",
- "do not print type and style hints in data file",
+ "-border", "-ax", "-ay", "-az", "-cd", "-cmap");
+ my @remarks = ("display this message",
+ "add charmm types to LAMMPS data file",
"add TIP3P water [default: 1 g/cc]",
"add (counter)ions using Na+ and Cl- [default: 0 mol/l]",
"recenter atoms",
@@ -71,14 +94,20 @@
"add border to all sides of simulation box [default: 0 A]",
"rotation around x-axis",
"rotation around y-axis",
- "rotation around z-axis"
+ "rotation around z-axis",
+ "use the 6-ring dihedral correction",
+ "generate the CMAP section"
);
my $notes;
$program = "charmm2lammps";
- $version = "1.8.3";
- $year = "2016";
- $add = 1;
+# $version = "1.8.2.5 beta"; # Modified by Xiaohu Hu, Dec 2009
+ $version = "1.8.2.6 beta"; # Modified by Robert Latour & Chris Lorenz, May 2013
+# $year = "2009"; # Modified by Xiaohu Hu, April 2009
+ $year = "2013"; # Modified by Robert Latour & Chris Lorenz, May 2013
+ $cmap = 0; # Added by Xiaohu Hu, May 2009
+ $cdihedral = 0; # Added by Xiaohu Hu, May 2009
+ $add = 0;
$water_dens = 0;
$ions = 0;
$info = 1;
@@ -112,7 +141,7 @@
foreach (@ARGV)
{
- if (substr($_, 0, 1) eq "-")
+ if (substr($_, 0, 1) eq "-") # if the first letter of the aguement is "-" = an option
{
my $k = 0;
my @tmp = split("=");
@@ -123,23 +152,24 @@
last if ($tmp[0] eq substr($_, 0 , length($tmp[0])));
++$k;
}
- $help = 1 if (!$k--); # -help
- $add = 0 if (!$k--); # -nohints
- $water_dens = ($tmp[1] ne "" ? $tmp[1] : 1) if (!$k--); # -water
- $ion_molar = abs($tmp[1]) if (!$k); # -ions
- $ions = 1 if (!$k--); # ...
- $center = 1 if (!$k--); # -center
- $info = 0 if (!$k--); # -quiet
- $pdb_ctrl = $switch if (!$k--); # -pdb_ctrl
- my $flag = $k--; # -l
- $L[0] = abs($tmp[1]) if (!($flag && $k--)); # -lx
- $L[1] = abs($tmp[1]) if (!($flag && $k--)); # -ly
- $L[2] = abs($tmp[1]) if (!($flag && $k--)); # -lz
- $border = abs($tmp[1]) if (!$k--); # -border
- @R = M_Dot(M_Rotate(0, $tmp[1]), @R) if (!$k--);# -ax
- @R = M_Dot(M_Rotate(1, $tmp[1]), @R) if (!$k--);# -ay
- @R = M_Dot(M_Rotate(2, $tmp[1]), @R) if (!$k--);# -az
- print("Warning: ignoring unknown command line flag: $tmp[0]\n");
+ $help = 1 if (!$k--);
+ $add = 1 if (!$k--);
+ $water_dens = ($tmp[1] ne "" ? $tmp[1] : 1) if (!$k--);
+ $ion_molar = abs($tmp[1]) if (!$k);
+ $ions = 1 if (!$k--);
+ $center = 1 if (!$k--);
+ $info = 0 if (!$k--);
+ $pdb_ctrl = $switch if (!$k--);
+ my $flag = $k--;
+ $L[0] = abs($tmp[1]) if (!($flag && $k--));
+ $L[1] = abs($tmp[1]) if (!($flag && $k--));
+ $L[2] = abs($tmp[1]) if (!($flag && $k--));
+ $border = abs($tmp[1]) if (!$k--);
+ @R = M_Dot(M_Rotate(0, $tmp[1]), @R) if (!$k--);
+ @R = M_Dot(M_Rotate(1, $tmp[1]), @R) if (!$k--);
+ @R = M_Dot(M_Rotate(2, $tmp[1]), @R) if (!$k--);
+ $cdihedral = 1 if (!$k--); # Added by Xiaohu Hu, May 2009
+ $cmap = 1 if (!$k--); # Added by Xiaohu Hu, May 2009
}
else
{
@@ -150,7 +180,7 @@
$water_dens = 1 if ($ions && !$water_dens);
if (($k<2)||$help)
{
- printf("\n%s v%s (c)%s by Pieter J. in \'t Veld for SNL\n\n",
+ printf("\n%s v%s (c)%s by Pieter J. in \'t Veld for SNL\nwith 6-ring dihedral correction and CMAP added by X. Hu, 2009\n\n",
$program, $version, $year);
printf("Usage:\n %s.pl [-option[=#] ..] forcefield project\n\n",$program);
printf("Options:\n");
@@ -161,7 +191,7 @@
printf("\nNotes:\n%s\n", $notes);
exit(-1);
}
- else { printf("\n%s v%s (c)%s\n\n", $program, $version, $year) if ($info); }
+ else { printf("%s v%s (c)%s\n\n", $program, $version, $year) if ($info); }
my $flag = Test($Parameters = "par_$forcefield.prm");
$flag |= Test($Topology = "top_$forcefield.rtf");
$flag |= Test($Pdb = "$project.pdb")
@@ -300,7 +330,7 @@
sub PSFConnectivity
{
- my $n = PSFGoto(bonds);
+ my $n = PSFGoto(bonds); # $n = the total number of bonds
return if (scalar(@nconnect));
printf("Info: creating connectivity\n") if ($info);
@@ -312,7 +342,6 @@
}
}
-
sub PSFDihedrals # hack to accomodate
{ # LAMMPS' way of calc
$idihedral = 0; # LJ 1-4 interactions
@@ -343,7 +372,6 @@
return $ndihedral;
}
-
sub CreatePSFIndex # make an index of id
{ # locations
my @psf_ids = ("!NATOM","!NBOND:","!NTHETA:","!NPHI:","!NIMPHI:");
@@ -363,26 +391,24 @@
}
}
-
- sub PSFGoto # goto $ident in <PSF>
+ sub PSFGoto # goto $ident in <PSF> and return the total number of $ident
{
CreatePSFIndex() if (!scalar(%PSFIndex));
my $id = shift(@_);
- my @n = split(" ", $PSFIndex{$id});
+ my @n = split(" ", $PSFIndex{$id}); # = 1 if the $ident is found
@PSFBuffer = ();
# return PSFDihedrals() if ($id eq "dihedrals");
if (!scalar(@n))
{
printf("Warning: PSF index for $id not found\n");
- seek(PSF, 0, SEEK_END);
+ seek(PSF, 0, SEEK_END); # set file-handle position to the EOF
return -1;
}
seek(PSF, $n[0], SEEK_SET);
return $n[1];
}
-
sub PSFGet
{
if ($dihedral_flag)
@@ -400,7 +426,7 @@
}
- sub PSFWrite
+ sub PSFWrite
{
my $items = shift(@_);
my $n = $items;
@@ -516,14 +542,11 @@
sub Markers
{
- my %markers = (
- NONBONDED => '0',
- BONDS => '1',
- ANGLES => '2',
- DIHEDRALS => '3',
- IMPROPERS => '4',
- IMPROPER => '4'
- );
+ my %markers;
+ my $n = 0;
+
+ foreach ("NONBONDED", "BONDS", "ANGLES", "DIHEDRALS", "IMPROPER") {
+ $markers{$_} = $n++; }
return %markers;
}
@@ -613,7 +636,7 @@
{ # <PARAMETERS>
my $mode = shift(@_); # bonded mode
return if (($mode>3)||($mode<0));
-
+
my $items = (2, 3, 4, 4)[$mode]; # items per entry
my $name = ("bond", "angle", "dihedral", "improper")[$mode];
my $read = 0;
@@ -688,7 +711,7 @@
sub SetScreeningFactor # set screening factor
{
- my $id = shift(@_);
+ my $id = shift(@_); # @_ has the form: ($variable, float no.)
my $value = shift(@_);
my $new = "";
@@ -702,7 +725,6 @@
$parms[$id] = $new;
}
-
sub CorrectDihedralParameters
{
my $n = PSFGoto(dihedrals);
@@ -713,15 +735,20 @@
my $first;
my $last;
- for (my $i=0; $i<$n; ++$i)
+ for (my $i=0; $i<$n; ++$i) # loop over all dihedrals
{
- my @bonded = PSFGet(4);
+ my @bonded = PSFGet(4);
my @tmp = ();
foreach (@bonded) { push(@tmp, $ids{$atom_types[$_]}); }
$id1 = $link{CreateID(@tmp)}-1;
$first = $bonded[0];
$last = $bonded[3];
+
if ($first>$last) { my $tmp = $first; $first = $last; $last = $tmp; }
+
+ # if the condition "$id2 = $hash{$hash_id = $first." ".$last}" is false, which means
+ # the id isn't in the hash, then it will be added, otherwise means this condition is
+ # true and the
if (($id2 = $hash{$hash_id = $first." ".$last}) eq "")
{
$hash{$hash_id} = $id1; # add id to hash
@@ -1010,7 +1037,7 @@
sub WriteLAMMPSHeader # print lammps header
{
- printf(LAMMPS "LAMMPS data file. CGCMM style. atom_style full. Created by $program v$version on %s\n", `date`);
+ printf(LAMMPS "Created by $program v$version on %s\n", `date`);
printf(LAMMPS "%12d atoms\n", $natoms);
printf(LAMMPS "%12d bonds\n", $nbonds);
printf(LAMMPS "%12d angles\n", $nangles);
@@ -1114,7 +1141,7 @@
{
my @xyz = V_Add(@p, @p_water[$i,$i+1,$i+2]);
@xyz = V_Add(@xyz, @Center) if (!$center);
- printf(LAMMPS "%8d %7d %5d %9.6g %11.8g %11.8g %11.8g%s\n",
+ printf(LAMMPS "%8d %7d %5d %9.6g %16.12g %16.12g %16.12g%s\n",
++$k, $res, $par[$j], $charge[$j], $xyz[0], $xyz[1],
$xyz[2], $add ? " # ".$types[$par[$j]-1] : "");
printf(PDB_CTRL "ATOM %6.6s %-4.4s %-3.3s %5.5s %3.3s ".
@@ -1164,7 +1191,7 @@
CRDGoto(atoms);
$net_charge = 0;
- printf(LAMMPS "Atoms # full\n\n") if ($n>0);
+ printf(LAMMPS "Atoms\n\n") if ($n>0);
for (my $i=0; $i<$n; ++$i)
{
my @crd = $pdb ? NextPDB2CRD() : split(" ", <CRD>);
@@ -1172,7 +1199,7 @@
my @xyz = MV_Dot(@R, @crd[-6, -5, -4]);
@xyz = V_Subtr(@xyz, @Center) if ($center);
if ($crd[-2]!=$res[1]) { ++$res[0]; $res[1] = $crd[-2]; }
- printf(LAMMPS "%8d %7d %5d %9.6g %11.7g %11.7g %11.7g%s\n", ++$k,
+ printf(LAMMPS "%8d %7d %5d %9.6g %16.12g %16.12g %16.12g%s\n", ++$k,
$res[0], $link{$atom_types[$k]}, $psf[6], $xyz[0], $xyz[1], $xyz[2],
$add ? " # ".$types[$link{$atom_types[$k]}-1] : "");
printf(PDB_CTRL "ATOM %6.6s %-4.4s %-4.4s %4.4s %3.3s ".
@@ -1198,7 +1225,6 @@
{
my $mode = shift(@_)+1;
my $header = ("Pair","Bond","Angle","Dihedral","Improper")[$mode];
- my $hint = ("lj/charmm/coul/long", "harmonic", "charmm", "charmm", "harmonic")[$mode];
my $n = (4, 2, 4, 4, 2)[$mode];
my $k = 0;
@@ -1212,7 +1238,7 @@
@parms = Delete(1, @parms) if ($mode==3);
}
return 0 if (!scalar(@parms));
- printf(LAMMPS "%s Coeffs # %s\n\n", $header, $hint);
+ printf(LAMMPS "%s Coeffs\n\n", $header);
for (my $i=0; $i<scalar(@parms); ++$i)
{
if ($parms[$i] ne "")
@@ -1222,7 +1248,7 @@
my @tmp = split(" ");
printf(LAMMPS "%8d", ++$k);
for (my $j=0; $j<$n; ++$j) {
- printf(LAMMPS " %10.7g", $j<scalar(@tmp) ? $tmp[$j] : 0); }
+ printf(LAMMPS " %16.12g", $j<scalar(@tmp) ? $tmp[$j] : 0); }
printf(LAMMPS "%s\n", $add ? " # ".$types[$i] : "");
}
} else { ++$k; }
@@ -1392,11 +1418,6 @@
CreateCorrectedPairCoefficients();
for (my $i=0; $i<scalar(@types); ++$i) { $types[$i] = $ids{$types[$i]}; }
$natom_types = WriteParameters(-1); # pairs
- if ($#types+1 > $natom_types) {
- print "Warning: $#types atom types present, but only $natom_types pair coeffs found\n";
- # reset to what is found while determining the number of atom types.
- $natom_types = $#types+1;
- }
$natoms = WriteAtoms();
$nbond_types = WriteParameters(0); # bonds
$nbonds = WriteBonded(0);
@@ -1428,15 +1449,29 @@
printf(LAMMPS "# Created by $program v$version on %s\n", `date`);
printf(LAMMPS "units real\n"); # general
printf(LAMMPS "neigh_modify delay 2 every 1\n\n");
+
+ printf(LAMMPS "boundary p p p\n\n");
printf(LAMMPS "atom_style full\n"); # styles
printf(LAMMPS "bond_style harmonic\n") if ($nbond_types);
printf(LAMMPS "angle_style charmm\n") if ($nangle_types);
printf(LAMMPS "dihedral_style charmm\n") if ($ndihedral_types);
printf(LAMMPS "improper_style harmonic\n\n") if ($nimproper_types);
- printf(LAMMPS "pair_style lj/charmm/coul/long 8 10\n");
+ printf(LAMMPS "# if cutoffs to be used for electrostatics, use pair_style lj/charmmfsw/coul/charmmfsh\n");
+ printf(LAMMPS "# and delete or comment out kspace_style\n");
+ printf(LAMMPS "pair_style lj/charmm/coul/long 8 12\n");
printf(LAMMPS "pair_modify mix arithmetic\n");
printf(LAMMPS "kspace_style pppm 1e-4\n\n");
- printf(LAMMPS "read_data $project.data\n\n"); # read data
+
+ if ($cmap) {
+ printf(LAMMPS "# Modify following lines to provide directory path cmap.data and 'project'.data files\n");
+ printf(LAMMPS "fix cmap all cmap /directoryPath/.../cmap36.data\n");
+ printf(LAMMPS "fix_modify cmap energy yes\n");
+ printf(LAMMPS "read_data /directoryPath/.../$project.data fix cmap crossterm CMAP\n\n");
+ }else{
+ printf(LAMMPS "# Modify following line to provide directory path for 'project'.data file\n");
+ printf(LAMMPS "read_data /directoryPath/.../$project.data\n\n"); # read data
+ }
+
if ($coefficients ne "") # corrected coeffs
{
foreach (split(":", $coefficients))
@@ -1446,16 +1481,15 @@
printf(LAMMPS "\n");
}
printf(LAMMPS "special_bonds charmm\n"); # invoke charmm
- printf(LAMMPS "thermo 1\n"); # set thermo style
- printf(LAMMPS "thermo_style multi\n");
- printf(LAMMPS "timestep 0.5\n\n"); # 0.5 ps time step
- printf(LAMMPS "minimize 0.0 0.0 1000 10000\n\n"); # take off the edge
printf(LAMMPS "fix 1 all nve\n");
printf(LAMMPS "fix 2 all shake 1e-6 500 0 m 1.0\n")
if ($shake eq ""); # shake all H-bonds
printf(LAMMPS "fix 2 all shake 1e-6 500 0 m 1.0 a %s\n",$shake)
if ($shake ne ""); # add water if present
printf(LAMMPS "velocity all create 0.0 12345678 dist uniform\n\n");
+ printf(LAMMPS "thermo 1\n"); # set thermo style
+ printf(LAMMPS "thermo_style multi\n");
+ printf(LAMMPS "timestep 0.5\n\n"); # 0.5 ps time step
printf(LAMMPS "restart 10 $project.restart1 $project.restart2\n");
printf(LAMMPS "dump 1 all atom 10 $project.dump\n");
printf(LAMMPS "dump_modify 1 image yes scale yes\n\n");
@@ -1463,6 +1497,972 @@
close(LAMMPS);
}
+ # ------------------ DESCRIPTION: sub DihedralCorrect6Ring ------------------ #
+ # #
+ # This subroutine is a subsequent correction of the dihedral 1-4 non-bonded #
+ # interaction scaling factor in the LAMMPS data file. The problem occurs in #
+ # dealing with carbohydrate systems, when some dihedrals outside of a 6-ring #
+ # are incorrectly assigned to the same dihedral type as dihedrals within a #
+ # 6-ring. Thus, those dihedrals outside of a 6-ring will be treated with a #
+ # 1-4 non-bonded interaction scaling factor of 0.5 instead of 1. #
+ # #
+ # By: Xiaohu Hu (hux2@ornl.gov) #
+ # #
+ # April 2009 #
+ # #
+ # --------------------------------------------------------------------------- #
+
+sub DihedralCorrect6Ring
+{
+ print "\nINITIATE DIHEDRAL CORRECTION...\n\n";
+ ## Variables for general data
+ # arrays
+ my @temp_data1;
+ my @temp_data2;
+ my @dihedral_coeffs;
+ my @dihedral_list;
+ my @raw_data;
+ my @temp1;
+ my @temp2;
+ my @temp3;
+ my @ring_dihe_list;
+ my @ring_dihetype_list;
+
+ # integers
+ my $counter1 = 0;
+ my $counter2 = 0;
+ my $net_ndihedral = 0;
+ my $net_ndihedral_types = 0;
+ my $splice_onset_dihe = 0;
+ my $splice_onset_dihe_coeff = 0;
+ my $n;
+ my $ntyp;
+
+ # matrix
+ my @dihedral_matrix;
+ my @dihedral_coeff_matrix;
+ my @new_dihedral_coeff_matrix;
+ my @new_dihedral_matrix;
+
+ ## Variables for dihedral matrix data
+ # "Dihedral Coeffs"
+ my $dihedral_type_c;
+ my $amp;
+ my $period;
+ my $equ_val;
+ my $scaling;
+
+ # "Dihedrals"
+ my $dihedral_no;
+ my $dihedral_type_l;
+ my $atom_1_no;
+ my $atom_2_no;
+ my $atom_3_no;
+ my $atom_4_no;
+
+# ------------- Reread the previously generated LAMMPS data file --------------------
+
+ open(LAMMPS, "< $project.data") or
+ die "\"sub DihedralCorrect6Ring\" cannot open \"$project.data!\n";
+ print "Analysing \"$project.data\"...\n\n";
+ @raw_data = <LAMMPS>;
+ close(LAMMPS);
+
+ # Find the number of dihedrals and dihedral types and the sections "Dihedrals"
+ # and "Dihedral Coeffs" in LAMMPS data file
+ foreach $line (@raw_data) {
+ $counter1++;
+ chomp($line);
+ if ($line =~ m/dihedrals/) {
+ ($n,$string) = split(" ",$line);
+ print "$n dihedrals\n";
+ }
+ if ($line =~ m/dihedral types/) {
+ ($ntyp,$string) = split(" ",$line);
+ print "$ntyp dihedral types\n";
+ }
+ if ($line =~ m/Dihedral Coeffs/) {
+ print "Section \"Dihedrals\" found\n";
+ $splice_onset_dihe_coeff = $counter1;
+ }
+ if ($line =~ m/Dihedrals/) {
+ print "Section \"Dihedral Coeffs\" found\n";
+ $splice_onset_dihe = $counter1;
+ }
+ }
+ if ($splice_onset_dihe_coeff == 0 and $splice_onset_dihe == 0) {
+ print "\nNo dihedral data in \"$project.data\", no dihedral correction necessary\n";
+ return;
+ }
+ elsif ($splice_onset_dihe_coeff == 0 or $splice_onset_dihe == 0) {
+ print "\nDihedral data incomplete! Dihedral correction impossible\n";
+ return;
+ }
+
+
+# --------------- Transform the raw data into matrices -----------------------
+
+ @temp_data1 = @temp_data2 = @raw_data;
+
+ #Store the section "Dihedral Coeffs" into a new list
+ @dihedral_coeffs = splice(@temp_data1,$splice_onset_dihe_coeff,$ntyp+1);
+
+ # Transfer the data from "@dihedral_coeffs" (an array of strings)
+ # into "@dihedral_coeff_matrix" (a 6 x $n matrix of integers)
+ for (@dihedral_coeffs) {
+ ($dihedral_type_c,
+ $amp,
+ $period,
+ $equ_val,
+ $scaling) = split(" ");
+
+ push(@dihedral_coeff_matrix,
+ [$dihedral_type_c,
+ $amp,
+ $period,
+ $equ_val,
+ $scaling]);
+ }
+
+ # Store the section "Dihedrals" into a new list
+ @dihedral_list = splice(@temp_data2,$splice_onset_dihe,$n+1);
+
+ # Transfer the data from "@dihedral_list" (an array of strings)
+ # into "@dihedral_matrix" (a 6 x $n matrix of integers)
+ for (@dihedral_list) {
+ ($dihedral_no,
+ $dihedral_type_l,
+ $atom_no_1,
+ $atom_no_2,
+ $atom_no_3,
+ $atom_no_4) = split(" ");
+
+ push(@dihedral_matrix,
+ [$dihedral_no,
+ $dihedral_type_l,
+ $atom_no_1,
+ $atom_no_2,
+ $atom_no_3,
+ $atom_no_4]);
+ }
+
+ for (my $i = 1; $i < $n; $i++) {
+ my $cur_type = ${$dihedral_matrix[$i]}[1];
+ if ($cur_type == 1 or
+ $cur_type == 16 or
+ $cur_type == 34 or
+ $cur_type == 46 or
+ $cur_type == 58 or
+ $cur_type == 64) {
+ push(@list,$cur_type);
+ }
+ }
+ @list = sort {$a <=> $b} @list;
+ #print "@list\n";
+ #print "Total: $#list\n";
+
+# ------------------ Reformat the matrices -------------------------------
+
+ # Loop the dihedral coefficient matrix and throw away all elements
+ # with a zero scaling factor (= entries with periodicity != 1)
+ for (my $i = 1; $i < $ntyp; $i++) {
+ my $current_sf = ${$dihedral_coeff_matrix[$i]}[4];
+ if ($current_sf != 0) {
+ push(@new_dihedral_coeff_matrix,
+ [${$dihedral_coeff_matrix[$i]}[0],
+ ${$dihedral_coeff_matrix[$i]}[1],
+ ${$dihedral_coeff_matrix[$i]}[2],
+ ${$dihedral_coeff_matrix[$i]}[3],
+ ${$dihedral_coeff_matrix[$i]}[4]]);
+ $net_ndihedral_types++;
+ }
+ }
+
+ # Remove the duplicated dihedrals from the @dihedral_matrix and save
+ # results into @new_dihedral_matrix
+ push(@new_dihedral_matrix,
+ [${$dihedral_matrix[1]}[0],
+ ${$dihedral_matrix[1]}[1],
+ ${$dihedral_matrix[1]}[2],
+ ${$dihedral_matrix[1]}[3],
+ ${$dihedral_matrix[1]}[4],
+ ${$dihedral_matrix[1]}[5]]);
+ $net_ndihedral = 1;
+ for (my $i = 2; $i < $n; $i++) {
+ if (${$dihedral_matrix[$i]}[2] != ${$dihedral_matrix[$i-1]}[2] or
+ ${$dihedral_matrix[$i]}[3] != ${$dihedral_matrix[$i-1]}[3] or
+ ${$dihedral_matrix[$i]}[4] != ${$dihedral_matrix[$i-1]}[4] or
+ ${$dihedral_matrix[$i]}[5] != ${$dihedral_matrix[$i-1]}[5]) {
+ push(@new_dihedral_matrix,
+ [${$dihedral_matrix[$i]}[0],
+ ${$dihedral_matrix[$i]}[1],
+ ${$dihedral_matrix[$i]}[2],
+ ${$dihedral_matrix[$i]}[3],
+ ${$dihedral_matrix[$i]}[4],
+ ${$dihedral_matrix[$i]}[5]]);
+ $net_ndihedral++;
+ }
+ }
+
+ # Print out the matrix
+ # my $ref_line;
+ # my $column;
+ # print "New dihedral list:\n";
+ # foreach $ref_line (@new_dihedral_matrix) {
+ # foreach $column (@$ref_line) {
+ # print "$column "
+ # }
+ # print "\n";
+ # }
+
+# --------------- Seach for the wrong scaling factors ----------------------------
+
+ # Loop through the dihedral matrix to determine the dihedrals within
+ # a 6-ring. Note there is some duplication in this approach due to
+ # processing already processed dihedrals. This will be taken care of
+ # later.
+ #
+ # NOTE: @ringlist contains the dihedrals types which corresponds to
+ # dihedrals within a 6-ring system.
+ #
+ my $n6ring = 0;
+ for (my $i = 1; $i < $net_ndihedral; $i++) {
+ my $current_i = ${$new_dihedral_matrix[$i]}[2];
+ my $current_l = ${$new_dihedral_matrix[$i]}[5];
+ for (my $j = $i + 1; $j < $net_ndihedral; $j++) {
+ if ( ($current_i == ${$new_dihedral_matrix[$j]}[2] and
+ $current_l == ${$new_dihedral_matrix[$j]}[5]) or
+ ($current_i == ${$new_dihedral_matrix[$j]}[5] and
+ $current_l == ${$new_dihedral_matrix[$j]}[2]) ) {
+ push(@temp2,${$new_dihedral_matrix[$i]}[0]);
+ push(@temp2,${$new_dihedral_matrix[$j]}[0]);
+ push(@temp3,${$new_dihedral_matrix[$i]}[1]);
+ push(@temp3,${$new_dihedral_matrix[$j]}[1]);
+ $n6ring++;
+ }
+ }
+ }
+
+ if ($n6ring == 0) {
+ print "\nNo dihedrals within 6-ring structure found. No correction necessary.\n";
+ return;
+ }
+
+ # Sort the lists according to the numerical order
+ @ring_dihe_list = sort {$a <=> $b} @temp2;
+ @ring_dihetype_list = sort {$a <=> $b} @temp3;
+
+ # Remove the dups
+ my %seen1;
+ for (my $i = 0; $i <= $#ring_dihe_list;) {
+ splice @ring_dihe_list, --$i, 1
+ if $seen1 {$ring_dihe_list[$i++]}++;
+ }
+
+ my %seen2;
+ for (my $i = 0; $i <= $#ring_dihetype_list;) {
+ splice @ring_dihetype_list, --$i, 1
+ if $seen1 {$ring_dihetype_list[$i++]}++;
+ }
+
+ print "6-ring dihedral types:\n";
+ print "@ring_dihetype_list\n";
+ print "6-ring dihedrals:\n";
+ print "@ring_dihe_list\n";
+
+ # Locate the wrong dihedrals in the dihedral list. Criteria to be wrong:
+ # if the type of the dihedral is equal to one from the list @ring_dihetype_list
+ # but not one from the @ring_dihe_list
+ my @errorlist;
+ my @errortypes;
+ my @raw_errortypes;
+ my $dihe_flag = 0;
+
+ for (my $i = 1; $i < $n; $i++) {
+ my $cur_dihe = ${dihedral_matrix[$i]}[0];
+ my $cur_type = ${dihedral_matrix[$i]}[1];
+
+ for (my $j = 0; $j <= $#ring_dihetype_list; $j++) {
+ if ($cur_type == $ring_dihetype_list[$j]) {
+ for (my $k = 0; $k <= $#ring_dihe_list; $k++) {
+ if ($cur_dihe == $ring_dihe_list[$k]) {
+ $dihe_flag++;
+ }
+ }
+ }
+ }
+
+ if ($dihe_flag == 0) {
+ for (my $j = 0; $j <= $#ring_dihetype_list; $j++) {
+ if ($cur_type == $ring_dihetype_list[$j]) {
+ push(@errorlist,$cur_dihe);
+ push(@raw_errortypes,$cur_type);
+ $counter2++;
+ }
+ }
+ }
+
+ $dihe_flag = 0;
+ }
+
+ if ($counter2 == 0) {
+ print "\nNo mis-assigned dihedrals found. No correction necessary.\n";
+ return;
+ }
+
+ print "mis-assigned dihedral/s found: $counter2\n";
+ print "@errorlist\n";
+ # print "@raw_errortypes\n";
+
+ # Sort the @errortypes and remove dups
+ @errortypes = sort {$a <=> $b} @raw_errortypes;
+ my %seen4;
+ for (my $i = 0; $i <= $#errortypes;) {
+ splice @errortypes, --$i, 1
+ if $seen4 {$errortypes[$i++]}++;
+ }
+
+ print "associated dihedral type/s\n";
+ print "@errortypes\n";
+
+# ------------ Add new dihedral types for the mis-assigned dihedrals -----------
+
+ print "\nWriting \"corrected_$project.data\"...\n\n";
+ open(REWRITE,"> corrected_$project.data")
+ or die "Can not write file \"corrected_$project.data\"!\n";
+
+ my $counter3 = 0;
+ my $fix_start = $splice_onset_dihe_coeff + $ntyp + 1;
+ my $new_ntyp = $ntyp + $#errortypes +1;
+
+ foreach $line (@raw_data) {
+ # update header information
+ if ($line =~ m/dihedral types/) {
+ $line =~ s/$ntyp/$new_ntyp/;
+ }
+
+ $counter3++;
+ printf(REWRITE "$line\n");
+ if ($counter3 == $fix_start) { last }
+ }
+
+ my @newtypes;
+ for (my $i = 0; $i <= $#errortypes; $i++) {
+ $ntyp++;
+ printf(REWRITE "%8d %10.7g %10d %10d 1\n",
+ $ntyp,
+ ${$dihedral_coeff_matrix[$errortypes[$i]]}[1],
+ ${$dihedral_coeff_matrix[$errortypes[$i]]}[2],
+ ${$dihedral_coeff_matrix[$errortypes[$i]]}[3]);
+ print "New dihedral type $ntyp added\n";
+ push(@newtypes,$ntyp);
+ }
+
+# ------------ Assign the wrong dihedrals with the new types ----------------
+
+ print "\nCorrecting the mis-assigned dihedrals...\n\n";
+
+ printf(REWRITE "$raw_data[$splice_onset_dihe - 2]\n");
+ printf(REWRITE "$raw_data[$splice_onset_dihe - 1]\n");
+
+ # Overwrite the wrong dihedrals in the dihedral list (section "Dihedrals")
+ my $counter3 = -1;
+ my $write_flag = 0;
+ my @temp_line;
+
+ for ($j = $splice_onset_dihe; $j <= $#raw_data; $j++) {
+ $counter3++;
+ for (my $i = 0; $i <= $#errorlist; $i++) {
+ if ($counter3 == $errorlist[$i]) {
+ @temp_line = split(" ",$raw_data[$j]);
+ for (my $k = 0; $k <= $#errortypes; $k++) {
+ if ($temp_line[1] == $errortypes[$k]) {
+ printf(REWRITE "%8d %7d %7d %7d %7d %7d\n",
+ ${$dihedral_matrix[$errorlist[$i]]}[0],
+ $newtypes[$k],
+ ${$dihedral_matrix[$errorlist[$i]]}[2],
+ ${$dihedral_matrix[$errorlist[$i]]}[3],
+ ${$dihedral_matrix[$errorlist[$i]]}[4],
+ ${$dihedral_matrix[$errorlist[$i]]}[5]);
+ print "Dihedral No. ${$dihedral_matrix[$errorlist[$i]]}[0] corrected\n";
+ $write_flag = 1;
+ }
+ }
+ }
+ }
+ if ($write_flag == 0) { printf(REWRITE "$raw_data[$j]\n");}
+ $write_flag = 0;
+ }
+
+ print "\nDONE!\n";
+
+ close(REWRITE);
+
+# End of the subroutine
+}
+
+# ----------------------- DESCRIPTION: sub CharmmCmap ------------------------ #
+# This subroutine add a new section "CMAP" to the LAMMPS data file, which #
+# a part of the implementation of "CHARMM CMAP" (see references) in LAMMPS. #
+# The section "CMAP" contains a list of dihedral ID pairs from adjecent #
+# peptide backtone dihedrals whose dihedral angles are corrresponding to PHI #
+# and PSI. (PHI: C--N--C_aphla_C and PSI: N--C_alpha--C--N) #
+# #
+# By: Xiaohu Hu (hux2@ornl.gov) #
+# May 2009 #
+# #
+# Modified May 2013 by: Robert Latour (latourr@clemson.edu) and #
+# Chris Lorenz (chris.lorenz@kcl.ac.uk #
+# #
+# References: #
+# - MacKerell, A.D., Jr., Feig, M., Brooks, C.L., III, Improved Treatment of #
+# Protein Backbone Conformational in Empirical Force Fields, J. Am. Chem. #
+# Soc. 126(2004): 698-699. #
+# - MacKerell, A.D., Jr., Feig, M., Brooks, C.L., III, Extending the Treatment #
+# of Backbone Energetics in Protein Force Fields: Limitations of Gas-Phase #
+# Quantum Mechnacis in Reproducing Protein Conformational Distributions in #
+# Molecular Dynamics Simulations, J. Comput. Chem. 25(2004): 1400-1415. #
+# ---------------------------------------------------------------------------- #
+
+sub CharmmCmap
+{
+ print "\nINITIATING CHARMM CMAP SUBROUTINE...\n\n";
+
+ # Reread and analyse $project.data
+ my @raw_data;
+ open(LAMMPS, "< $project.data") or
+ die "\"sub CharmmCmap()\" cannot open \"$project.data!\n";
+ print "Analyzing \"$project.data\"...\n\n";
+ @raw_data = <LAMMPS>;
+ close(LAMMPS);
+
+ # Locate and extract the sections "Masses" and "Atoms"
+ my $line_number = 0;
+ # Header infos, 0 by default
+ my $natom_types = 0;
+ my $natom_number = 0;
+ my $ndihedral_number = 0;
+ my $temp_string;
+ # splice points, 0 by default
+ my $splice_onset_masses = 0;
+ my $splice_onset_atoms = 0;
+ my $splice_onset_dihedrals = 0;
+
+ foreach my $line (@raw_data) {
+ $line_number++;
+ chomp($line);
+ # Extract useful informations from the header
+ if ($line =~ m/atom types/) {
+ ($natom_types,$temp_string) = split(" ",$line);
+ if ($natom_types == 0) {
+ die "\nError: Number of atom types is 0!\n";
+ }
+ print "Total atom types: $natom_types\n";
+ }
+ if ($line =~ m/atoms/) {
+ ($natom_number,$temp_string) = split(" ",$line);
+ if ($natom_number == 0) {
+ die "\nError: Number of atoms is 0!\n";
+ }
+ print "Total atoms: $natom_number\n";
+ }
+ if ($line =~ m/dihedrals/) {
+ ($ndihedral_number,$temp_string) = split(" ",$line);
+ if ($ndihedral_number == 0) {
+ die "\nError: Number of dihedrals is 0\n";
+ }
+ print "Total dihedrals: $ndihedral_number\n";
+ }
+ # Locate and data from sections "Masses", "Atoms" and "Dihedrals"
+ if ($line =~ m/Masses/) {
+ $splice_onset_masses = $line_number + 1;
+ if ($splice_onset_masses-1 == 0) {
+ die "\nError: Can not find the section \"Masses\"\n";
+ }
+ print "Section \"Masses\" found: line $splice_onset_masses\n";
+ }
+ if ($line =~ m/Atoms/) {
+ $splice_onset_atoms = $line_number +1;
+ if ($splice_onset_atoms-1 == 0) {
+ die "\nError: Can not find the section \"Atoms\"\n";
+ }
+ print "Section \"Atoms\" found: line $splice_onset_atoms\n";
+ }
+ if ($line =~ m/Dihedrals/) {
+ $splice_onset_dihedrals = $line_number + 1;
+ if ($splice_onset_dihedrals-1 == 0) {
+ die "\nError: Can not find the section \"Dihedrals\"\n";
+ }
+ print "Section \"Dihedrals\" found: line $splice_onset_dihedrals\n";
+ }
+ }
+
+ print "\nGenerating PHI/PSI dihedral pair list...\n\n";
+
+ my @temp1 = @raw_data;
+ my @temp2 = @raw_data;
+ my @temp3 = @raw_data;
+
+ # Extract the section "Masses", "Atoms" and "Dihedrals"
+ my @temp_masses_data = splice(@temp1,$splice_onset_masses,$natom_types);
+ my @temp_atoms_data = splice(@temp2,$splice_onset_atoms,$natom_number);
+ my @temp_dihedrals_data = splice(@temp3,$splice_onset_dihedrals,$ndihedral_number);
+
+ # Store @temp_masses_dat into a matrix
+ my @masses_matrix;
+ my $atom_type;
+ my $mass;
+ for (@temp_masses_data) {
+ ($atom_type, $mass) = split(" ");
+ push(@masses_matrix,[$atom_type,$mass]);
+ }
+
+ # Store @temp_atoms_data into a matrix
+ my @atoms_matrix;
+ my $atom_ID;
+ my $molecule_ID;
+ my $atype;
+ my $charge;
+ my $atom_x_coor;
+ my $atom_y_coor;
+ my $atom_z_coor;
+ for (@temp_atoms_data) {
+ ($atom_ID,$molecule_ID,$atype,$charge,$atom_x_coor,$atom_y_coor,$atom_z_coor) = split(" ");
+ push(@atoms_matrix,
+ [$atom_ID,$molecule_ID,$atype,$charge,$atom_x_coor,$atom_y_coor,$atom_z_coor]);
+ }
+
+ # Store @temp_dihedrals_data into a matrix
+ my @dihedrals_matrix;
+ my $dihedral_ID;
+ my $dihedtal_type;
+ my $dihe_atom1;
+ my $dihe_atom2;
+ my $dihe_atom3;
+ my $dihe_atom4;
+ for (@temp_dihedrals_data) {
+ ($dihedral_ID,$dihedral_type,$dihe_atom1,$dihe_atom2,$dihe_atom3,$dihe_atom4) = split(" ");
+ push(@dihedrals_matrix,
+ [$dihedral_ID,$dihedral_type,$dihe_atom1,$dihe_atom2,$dihe_atom3,$dihe_atom4]);
+ }
+
+ # Find out and extract the peptide backbone dihedrals
+ #
+ # Definitions of peptide backbone dihedrals
+ #
+ # For dihedral angle PHI: C--N--CA--C
+ # For dihedral angle PSI: N--CA--C--N
+ #
+ # ---------------------------------------------------------
+ # atom | mass |partial charge| amino-acid
+ # ---------------------------------------------------------
+ # C | 12.011 | 0.51 | all except GLY and PRO
+ # N | 14.007 | -0.29 | PRO
+ # N | 14.007 | -0.47 | all except PRO
+ # CA | 12.011 | 0.07 | all except GLY and PRO
+ # CA | 12.011 | -0.02 | GLY
+ # CA | 12.011 | 0.02 | PRO
+ # ---------------------------------------------------------
+ #
+ # Peptide backbone
+ # ...
+ # /
+ # O=C
+ # \
+ # N-H
+ # / -----> PHI (C-N-CA-C)
+ # H-CA-R
+ # \ -----> PSI (N-CA-C-N)
+ # C=O
+ # /
+ # H-N
+ # \
+ # ...
+ #
+ # Criteria to be a PHI/PSI dihedral pair:
+ # 1. Atoms have to match with the mass/charge constellations as
+ # defined above.
+ # 2. The atoms N--CA--C needs to be covalently bonded with each
+ # other.
+
+ # Find which types do C, N and CA correspond to and store them
+ # in lists
+ my $mass_carbon = 12.011;
+ my $mass_nitrogen = 14.007;
+
+ my @carbon_list;
+ my @nitrogen_list;
+ my $carbon_counter = 0;
+ my $nitrogen_counter = 0;
+
+ for (my $i = 0; $i < $natom_types; $i++) {
+ if (${$masses_matrix[$i]}[1] == $mass_carbon) {
+ push(@carbon_list,${$masses_matrix[$i]}[0]);
+ $carbon_counter++;
+ }
+ if (${$masses_matrix[$i]}[1] == $mass_nitrogen) {
+ push(@nitrogen_list,${$masses_matrix[$i]}[0]);
+ $nitrogen_counter++;
+ }
+ }
+ # Quit if no carbons or nitrogens
+ if ($carbon_counter == 0 or $nitrogen_counter == 0) {
+ if ($carbon_counter == 0) {
+ print "No carbon atoms exist in the system\n";
+ }
+ if ($nitrogen_counter == 0) {
+ print "No nitrogen atoms exist in the system\n";
+ }
+ print "CMAP usage impossible\n";
+ return;
+ }
+
+ print "Carbon atom type/s: @carbon_list\n";
+ print "Nitrogen atom type/s: @nitrogen_list\n";
+
+ # Determine the atom types of C, CA and N
+
+ # Charges of the backbone atoms
+ my $charge_C = 0.51;
+ my $charge_CA = 0.07;
+ my $charge_N = -0.47;
+
+ # Special setting for PRO
+ my $charge_N_PRO = -0.29;
+ my $charge_CA_PRO = 0.02;
+
+ # Special setting for GLY
+ my $charge_CA_GLY = -0.02;
+
+ # Peptide backbone atom types
+ my $C_type;
+ my $CA_type;
+ my $CA_GLY_type;
+ my $CA_PRO_type;
+ my $N_type;
+ my $N_PRO_type;
+
+ my $C_counter = 0;
+ my $CA_counter = 0;
+ my $CA_GLY_counter = 0;
+ my $CA_PRO_counter = 0;
+ my $N_counter = 0;
+ my $N_PRO_counter = 0;
+
+ my $C_flag = 0;
+
+ for (my $i = 0; $i <= $natom_number; $i++) {
+ my $cur_type = ${$atoms_matrix[$i]}[2];
+ my $cur_charge = ${$atoms_matrix[$i]}[3];
+ for (my $j = 0; $j <= $#carbon_list; $j++) {
+ if ($cur_type == $carbon_list[$j]) {
+ $C_flag = 1;
+ if ($cur_charge == $charge_C) {
+ $C_type = $cur_type;
+ $C_counter++;
+ }
+ if ($cur_charge == $charge_CA) {
+ $CA_type = $cur_type;
+ $CA_counter++;
+ }
+ if ($cur_charge == $charge_CA_GLY) {
+ $CA_GLY_type = $cur_type;
+ $CA_GLY_counter++;
+ }
+ if ($cur_charge == $charge_CA_PRO) {
+ $CA_PRO_type = $cur_type;
+ $CA_PRO_counter++;
+ }
+ }
+ }
+ if ($C_flag == 0) {
+ for (my $k = 0; $k <= $#nitrogen_list; $k++) {
+ if ($cur_type == $nitrogen_list[$k]) {
+ if ($cur_charge == $charge_N) {
+ $N_type = $cur_type;
+ $N_counter++;
+ }
+ if ($cur_charge == $charge_N_PRO) {
+ $N_PRO_type = $cur_type;
+ $N_PRO_counter++;
+ }
+ }
+ }
+ }
+ $C_flag = 0;
+ }
+
+ # Quit if one of the atom types dosen't exist
+ if ( $C_counter == 0 or
+ ($CA_counter == 0 and $CA_GLY_counter == 0 and $CA_PRO_counter == 0) or
+ ($N_counter == 0 and $N_PRO_counter == 0) ) {
+ if ($C_counter == 0) {
+ print "\nCannot find the peptide backbone C atom type\n";
+ }
+ if ($CA_counter == 0 and $CA_GLY_counter == 0 and $CA_PRO_counter == 0) {
+ print "\nCannot find the peptide backbone C-alpha atom type\n";
+ }
+ if ($N_counter == 0 and $N_PRO_counter == 0) {
+ print "\nCannot find the peptide backbone N atom type\n";
+ }
+ print "CMAP usage impossible\n";
+ return;
+ }
+
+ print "Peptide backbone carbon type: $C_type\n";
+ print "Alpha-carbon type: $CA_type\n" if ($CA_counter > 0);
+ print "Alpha-carbon type (GLY): $CA_GLY_type\n" if ($CA_GLY_counter > 0);
+ print "Alpha-carbon type (PRO): $CA_PRO_type\n" if ($CA_PRO_counter > 0);
+ print "Peptide backbone nitrogen type: $N_type\n" if ($N_counter >0);
+ print "Peptide backbone nitrogen type (PRO): $N_PRO_type\n" if ($N_PRO_counter > 0);
+
+ # Loop through the dihedral list to find the PHI- and PSI-dihedrals
+ my @PHI_dihedrals;
+ my @PSI_dihedrals;
+ my $PHI_counter = 0;
+ my $PSI_counter = 0;
+
+ for (my $i = 0; $i < $ndihedral_number; $i++) {
+ my $cur_dihe_ID = ${dihedrals_matrix[$i]}[0];
+ my $cur_atom1_type = ${atoms_matrix[${dihedrals_matrix[$i]}[2]-1]}[2];
+ my $cur_atom2_type = ${atoms_matrix[${dihedrals_matrix[$i]}[3]-1]}[2];
+ my $cur_atom3_type = ${atoms_matrix[${dihedrals_matrix[$i]}[4]-1]}[2];
+ my $cur_atom4_type = ${atoms_matrix[${dihedrals_matrix[$i]}[5]-1]}[2];
+
+ next if (${dihedrals_matrix[$i]}[2] == ${dihedrals_matrix[$i-1]}[2] and
+ ${dihedrals_matrix[$i]}[3] == ${dihedrals_matrix[$i-1]}[3] and
+ ${dihedrals_matrix[$i]}[4] == ${dihedrals_matrix[$i-1]}[4] and
+ ${dihedrals_matrix[$i]}[5] == ${dihedrals_matrix[$i-1]}[5]);
+
+ # Determine PHI-dihedrals; If C-CA-N-C or C-N-CA-C, then save it in a list
+ if ($cur_atom1_type == $C_type and $cur_atom4_type == $C_type) {
+ if ( ( ($cur_atom2_type == $CA_type or
+ $cur_atom2_type == $CA_GLY_type or
+ $cur_atom2_type == $CA_PRO_type) and
+ ($cur_atom3_type == $N_type or
+ $cur_atom3_type == $N_PRO_type) ) or
+ ( ($cur_atom3_type == $CA_type or
+ $cur_atom3_type == $CA_GLY_type or
+ $cur_atom3_type == $CA_PRO_type) and
+ ($cur_atom2_type == $N_type or
+ $cur_atom2_type == $N_PRO_type) ) ) {
+ push (@PHI_dihedrals,$cur_dihe_ID);
+ $PHI_counter++;
+ }
+ }
+
+ # Determin PSI-dihedrals; If N-CA-C-N or N-C-CA-N (N can be both normal N or N proline),
+ # then save it in a list
+ if ( ($cur_atom1_type == $N_type and $cur_atom4_type == $N_type) or
+ ($cur_atom4_type == $N_PRO_type and $cur_atom1_type == $N_PRO_type) or
+ ($cur_atom1_type == $N_type and $cur_atom4_type == $N_PRO_type) or
+ ($cur_atom4_type == $N_type and $cur_atom1_type == $N_PRO_type) ) {
+ if ( ( ($cur_atom2_type == $CA_type or
+ $cur_atom2_type == $CA_GLY_type or
+ $cur_atom2_type == $CA_PRO_type) and
+ $cur_atom3_type == $C_type) or
+ ( ($cur_atom3_type == $CA_type or
+ $cur_atom3_type == $CA_GLY_type or
+ $cur_atom3_type == $CA_PRO_type) and
+ $cur_atom2_type == $C_type) ) {
+ push (@PSI_dihedrals,$cur_dihe_ID);
+ $PSI_counter++;
+ }
+ }
+ }
+
+ # Quit if no PHI or PSI dihedrals
+ if ($PHI_counter == 0 or $PSI_counter ==0) {
+ if ($PHI_counter == 0) {
+ print "Can not find the PHI backbone dihedrals\n";
+ }
+ if ($PSI_counter ==0) {
+ print "Can not find the PSI backbone dihedrals\n";
+ }
+ print "CMAP usage impossible\n";
+ return;
+ }
+
+ # Construct the PHI/PSI diheral pair list
+ #
+ # The algorithm:
+ # _____
+ # | |
+ # 1--2--3--4 PHI-dihedral
+ # 4--3--2--1
+ # --C--N-CA--C--N-- Peptide backbone
+ # 1--2--3--4
+ # 4--3--2--1 PSI-dihedral
+ # |_____|
+ #
+ # For a certain PHI dihedral, following conditions have to be met:
+ #
+ # PHI PSI
+ # If (2--3--4) = (1--2--3)
+ # or
+ # if (2--3--4) = (4--3--2)
+ # or
+ # if (3--2--1) = (1--2--3)
+ # or
+ # if (3--2--1) = (4--3--2),
+ #
+ # then these 2 dihedrals are a PHI/PSI pair. If a pair is found, the
+ # dihedral IDs will be stored in "@PHI_PSI_matrix".
+
+ my @PHI_PSI_matrix;
+ my $crossterm_CA_charge;
+ my $crossterm_type;
+ my $crossterm_counter = 0;
+ my $crossterm_type1_flag = 0;
+ my $crossterm_type2_flag = 0;
+ my $crossterm_type3_flag = 0;
+ my $crossterm_type4_flag = 0;
+ my $crossterm_type5_flag = 0;
+ my $crossterm_type6_flag = 0;
+
+ for (my $i = 0; $i <= $#PHI_dihedrals; $i++) {
+ my $cur_PHI_dihe = ${dihedrals_matrix[$PHI_dihedrals[$i]-1]}[0];
+ my $phi1 = ${dihedrals_matrix[$PHI_dihedrals[$i]-1]}[2];
+ my $phi2 = ${dihedrals_matrix[$PHI_dihedrals[$i]-1]}[3];
+ my $phi3 = ${dihedrals_matrix[$PHI_dihedrals[$i]-1]}[4];
+ my $phi4 = ${dihedrals_matrix[$PHI_dihedrals[$i]-1]}[5];
+ for (my $j = 0; $j <= $#PSI_dihedrals; $j++) {
+ my $cur_PSI_dihe = ${dihedrals_matrix[$PSI_dihedrals[$j]-1]}[0];
+ my $psi1 = ${dihedrals_matrix[$PSI_dihedrals[$j]-1]}[2];
+ my $psi2 = ${dihedrals_matrix[$PSI_dihedrals[$j]-1]}[3];
+ my $psi3 = ${dihedrals_matrix[$PSI_dihedrals[$j]-1]}[4];
+ my $psi4 = ${dihedrals_matrix[$PSI_dihedrals[$j]-1]}[5];
+ if ( ($phi2 == $psi1 and $phi3 == $psi2 and $phi4 == $psi3) or
+ ($phi2 == $psi4 and $phi3 == $psi3 and $phi4 == $psi2) or
+ ($phi3 == $psi1 and $phi2 == $psi2 and $phi1 == $psi3) or
+ ($phi3 == $psi4 and $phi2 == $psi3 and $phi1 == $psi2) ) {
+
+ # Find out to which amino acid the cross-term belongs
+
+ if ($phi3 == $psi2 or $phi3 == $psi3) {
+ $crossterm_CA_charge = ${atoms_matrix[${dihedrals_matrix[$PHI_dihedrals[$i]-1]}[4]-1]}[3];
+ }
+ if ($phi2 == $psi2 or $phi2 == $psi3) {
+ $crossterm_CA_charge = ${atoms_matrix[${dihedrals_matrix[$PHI_dihedrals[$i]-1]}[3]-1]}[3];
+ }
+
+ # Def. the type of the crossterm per cmap.data file; If C_alpha of the crossterm is
+ # - ALA type, then $crossterm_type = 1;
+ # - ALA-PRO (ALA is the current AA), then $crossterm_type = 2;
+ # - PRO type, then $crossterm_type = 3;
+ # - PRO-PRO (First PRO is the current AA), then $crossterm_type = 4;
+ # - GLY type, then $crossterm_type = 5;
+ # - GLY-PRO (GLY is the current AA), then $crossterm_type = 6;
+
+ if ($crossterm_CA_charge == $charge_CA) { $crossterm_type = 1; $crossterm_type1_flag = 1; }
+ if ($crossterm_CA_charge == $charge_CA_GLY) { $crossterm_type = 5; $crossterm_type5_flag = 1; }
+ if ($crossterm_CA_charge == $charge_CA_PRO) {
+ $crossterm_type = 3; $crossterm_type3_flag = 1;
+ # Checking the last crossterm, re-assign the last crossterm type if needed
+ if ($crossterm_counter-1 >= 0 and $PHI_PSI_matrix[$crossterm_counter-1][0] == 1) {
+ $PHI_PSI_matrix[$crossterm_counter-1][0] = 2;
+ $crossterm_type2_flag = 1;
+ }
+ if ($crossterm_counter-1 >= 0 and $PHI_PSI_matrix[$crossterm_counter-1][0] == 3) {
+ $PHI_PSI_matrix[$crossterm_counter-1][0] = 4;
+ $crossterm_type4_flag = 1;
+ }
+ if ($crossterm_counter-1 >= 0 and $PHI_PSI_matrix[$crossterm_counter-1][0] == 5) {
+ $PHI_PSI_matrix[$crossterm_counter-1][0] = 6;
+ $crossterm_type6_flag = 1;
+ }
+ }
+ push(@PHI_PSI_matrix,[$crossterm_type,$phi1,$phi2,$phi3,$phi4,$psi4]);
+ $crossterm_counter++;
+
+ $crossterm_CA_charge = 0;
+ $crossterm_type = 0;
+ }
+ }
+ }
+
+ # Check whether the amino acid at the C-terminus is a PRO or not. If yes, the type of the last crossterm
+ # should be set to its X-PRO form instead of X, where X is ALA, PRO, or GLY. X-PRO form = X type + 1.
+
+ my @pdb_data;
+ open(PDB,"< $project.pdb")
+ or die "WARNING: Cannot open file \"$project.pdb\"! (required if the -cmap option is used)\n";
+ @pdb_data = <PDB>;
+ close(PDB);
+
+ my @ter_line;
+ my $ter_AA_type = 0;
+ my $ter_flag = 0;
+ foreach $line (@pdb_data) {
+ if ($line =~ m/TER/) {
+ @ter_line = split(" ",$line);
+ $ter_AA_type = $ter_line[2];
+ print "Terminal amino acid type is: $ter_AA_type\n";
+ $ter_flag = 1;
+ }
+ }
+ if ($ter_flag == 0) {
+ print "\n*** ERROR IN THE PDB FILE: ***\n";
+ print "In order for the CMAP section to be generated, the pdb file must \n";
+ print "identify the C-terminus amino acid in the file with 'TER'. \n";
+ print "This line is missing from the pdb file that was used.\n";
+ print "To correct this problem, open the pdb file in an editor,\n";
+ print "find the last atom of the last amino acid residue in the peptide\n";
+ print "chain and insert the following line immediately after that atom:\n";
+ print " 'TER <#1> <RES> <#2>' \n";
+ print "where '<#1> is the next atom number, <RES> is the three letter amino\n";
+ print "acid abbreviation for that amino acid, and <#2> is the molecule number\n";
+ print "of the terminal amino acid residue.\n\n";
+ print "For example, if the last atom of the last amino acid in the peptide\n";
+ print "sequence is listed in the pdb file as:\n\n";
+ print " 'ATOM 853 O GLU P 56 12.089 -1.695 -6.543 1.00 1.03 PROA'\n\n";
+ print "you would insert the following line after it:\n\n";
+ print " 'TER 854 GLU 56'\n\n";
+ print "If any additional atoms are listed in the pdb file (e.g., water, ions)\n";
+ print "after this terminal amino acid residue, their atom numbers and\n";
+ print "molecule numbers must be incremented by 1 to account for the new line\n";
+ print "that was inserted.\n\n";
+ die "Error: No terminating atom designated in pdb file! See above note to correct problem.\n\n";
+ }
+
+ if ($ter_AA_type eq PRO) {
+ $PHI_PSI_matrix[$crossterm_counter-1][0] = $PHI_PSI_matrix[$crossterm_counter-1][0]+1;
+ }
+
+ # Print out PHI/PSI diheral pair list
+ my $pair_counter = 0;
+ # Don't presently use $ncrosstermtypes but have this available if wish to print it out
+ my $ncrosstermtypes = $crossterm_type1_flag + $crossterm_type2_flag + $crossterm_type3_flag +
+ $crossterm_type4_flag + $crossterm_type5_flag + $crossterm_type6_flag;
+ print "\nWriting \"$project.data\" with section \"CMAP crossterms\" added at the end.\n";
+
+ # Writing the new lammps data file
+ open(REWRITE,"> $project.data")
+ or die "Cannot write file \"$project.data\"!\n";
+ foreach $line (@raw_data) {
+ printf(REWRITE "$line\n");
+ if ($line =~ m/impropers/) {
+ printf(REWRITE "%12d crossterms\n", $crossterm_counter);
+ }
+ }
+ printf(REWRITE "CMAP\n\n");
+
+ my $ref_line;
+ my $column;
+ foreach $ref_line (@PHI_PSI_matrix) {
+ $pair_counter++;
+ printf(REWRITE "%8d",$pair_counter);
+ foreach $column (@$ref_line) {
+ printf(REWRITE " %7d",$column);
+ }
+ printf(REWRITE "\n");
+ }
+ close(REWRITE);
+
+ print "\nDone!\n\n";
+
+# End of the CharmmCmap subroutine
+}
# main
@@ -1470,4 +2470,6 @@
WriteData();
WriteLAMMPSInput();
printf("Info: conversion complete\n\n") if ($info);
+ DihedralCorrect6Ring() if ($cdihedral);
+ CharmmCmap() if ($cmap);